Areas of expertise

• Receptors And Membrane Biology 060110
• Structural Biology (Incl. Macromolecular Modelling) 060112
• Theoretical And Computational Chemistry 0307
• Biomolecular Modelling And Design 030402
• Bioinformatics 060102

Publications

• Wilson, K, Fairweather, S, Macdermott-Opeskin, H et al. 2021, 'The role of plasmalogens, Forssman lipids, and sphingolipid hydroxylation in modulating the biophysical properties of the epithelial plasma membrane', Journal of Chemical Physics, vol. 154, no. 9.
• Fairweather, S, Gupta, V, Chitsaz, M et al. 2021, 'Coordination of Substrate Binding and Protonation in the N. gonorrhoeae MtrD Efflux Pump Controls the Functionally Rotating Transport Mechanism', ACS Infectious Diseases, vol. 7, no. 6, pp. 1833-1847.
• Wilson, K, Mostyn, S, Frangos, Z et al. 2021, 'The allosteric inhibition of glycine transporter 2 by bioactive lipid analgesics is controlled by penetration into a deep lipid cavity', Journal of Biological Chemistry, vol. 296, pp. 1-12.
• Bhaskaran, A, Aitken, H, Xiao, Z et al. 2021, 'Enzyme inspired polymer functionalized with an artificial catalytic triad', Polymer, vol. 225, pp. 1-5.
• Neville, S, Sjohamn, J, Watts, J et al. 2021, 'The structural basis of bacterial manganese import', Science Advances, vol. 7, no. 32.
• Ou, A, Schmidberger, J, Wilson, K et al. 2020, 'High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition', Nucleic Acids Research, vol. 48, no. 10, pp. 5766-5776.
• Wilson, K, Wang, L, Macdermott-Opeskin, H et al. 2020, 'The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane', Australian Journal of Chemistry, vol. 73, no. 3, pp. 85-95.
• Macdermott-Opeskin, H, McDevitt, C & O'Mara, M 2020, 'Comparing Nonbonded Metal Ion Models in the Divalent Cation Binding Protein PsaA', Journal of Chemical Theory and Computation (JCTC), vol. 16, no. 3, pp. 1913-1923.
• Wilson, K, Macdermott-Opeskin, H, Riley, E et al. 2020, 'Understanding the Link between Lipid Diversity and the Biophysical Properties of the Neuronal Plasma Membrane', Biochemistry, vol. 59, no. 33, pp. 3010-3018.
• Rawling, T, Macdermott-Opeskin, H, Roseblade, A et al. 2020, 'Aryl urea substituted fatty acids: A new class of protonophoric mitochondrial uncoupler that utilises a synthetic anion transporter', Chemical Science, vol. 11, no. 47, pp. 12677-12685.
• Carey Hulyer, A, Briggs, D, O'Mara, M et al. 2020, 'Cross-linking, DEER-spectroscopy and molecular dynamics confirm the inward facing state of P-glycoprotein in a lipid membrane', Journal of Structural Biology, vol. 211, pp. 1-14.
• Nothling, M, Xiao, Z, Hill, N et al 2020, 'A multifunctional surfactant catalyst inspired by hydrolases', Science Advances, vol. 6, no. 14, pp. -.
• Schumann-Gillett, A, Blyth, M & O'Mara, M 2019, 'Is protein structure enough? A review of the role of lipids in SLC6 transporter function', Neuroscience Letters, vol. 700, pp. 64-69.
• Schumann-Gillett, A & O'Mara, M 2019, 'Lipid-Based Inhibitors Act Directly on GlyT2', A C S Chemical Neuroscience, vol. 10, no. 3, pp. 1668-1678.
• Chiou, T, Long, P, Schumann-Gillett, A et al 2019, 'Mutation p.R356Q in the collybistin phosphoinositide binding site is associated with mild intellectual disability', Frontiers in Molecular Neuroscience, vol. 12, pp. 1-13.
• Mostyn, S, Wilson, K, Schumann-Gillett, A et al. 2019, 'Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics', eLife, vol. 8, pp. 1-22.
• Chitsaz, M, Booth, L, Blyth, M et al. 2019, 'Multidrug Resistance in Neisseria gonorrhoeae: Identification of Functionally Important Residues in the MtrD Efflux Protein', mBio, vol. 10, no. 6, pp. 1-14.
• Schumann-Gillett, A, Mark, A, Deplazes, E et al 2018, 'A potential new, stable state of the E-cadherin strand-swapped dimer in solution', European Biophysics Journal, vol. 47, no. 1, pp. 59-67pp.
• Schumann-Gillett, A & O'Mara, M 2018, 'The effects of oxidised phospholipids and cholesterol on the biophysical properties of POPC bilayers', Biochimica et Biophysica Acta: Biomembranes, vol. 1861, no. 1, pp. 210-219.
• Condic-Jurkic, K, Subramanian, N, Mark, A et al 2018, 'The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment', PLOS ONE (Public Library of Science), vol. 13, no. 1, pp. 24pp.
• Steinbeck, J, O'Mara, M, Ross, I et al 2017, 'Thylakoid Ultrastructure: Visualizing the Photosynthetic Machinery', in Hippler M. (ed.), Chlamydomonas: Biotechnology and Biomedicine, Springer, Berlin, pp. 149-191.
• Mitchell, J & O'Mara, M 2017, 'Capturing the Dynamics of a Spring-Loaded Protein', Structure, vol. 25, no. 7, pp. 963-964.
• Anandan, A, Evans, G, Condic-Jurkic, K et al 2017, 'Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 9, pp. 2218-2223.
• Nothling, M, Ganesan, A, Condic-Jurkic, K et al 2017, 'Simple Design of an Enzyme-Inspired Supported Catalyst Based on a Catalytic Triad', Chem, vol. 2, no. 5, pp. 732-745pp.
• Kretzmann, J, Ho, D, Evans, C et al. 2017, 'Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA', Chemical Science, vol. 8, no. 4, pp. 2923-2930.
• Mitchell, J, Zhang, W, Herde, M et al 2017, 'Method for Developing Optical Sensors Using a Synthetic Dye-Fluorescent Protein FRET Pair and Computational Modeling and Assessment', in Viktor Stein (ed.), Synthetic Protein Switches : Methods and Protocols, Humana Press, New York, pp. 89-100.
• Carland, J, Thomas, M, Mostyn, S et al 2017, 'Molecular Determinants for Substrate Interactions with the Glycine Transporter GlyT2', A C S Chemical Neuroscience, vol. 9, no. 3, pp. 603-614pp.
• M Thomas, T Anglim Lagones, M Judd, Morshedi, M, O'Mara, M & White, N 2017, 'Hydrogen bond-Driven Self-Assembly between Amidinium Cations and Carboxylate Anions: A Combined Molecular Dynamics, NMR Spectroscopy, and Single Crystal X-ray Diffraction Study', Chemistry - An Asian Journal, vol. 12, no. 13, pp. 1587-1597.
• Mittra, R, Pavy, M, Subramanian, N et al 2017, 'Location of contact residues in pharmacologically distinct drug binding sites on P-glycoprotein', Biochemical Pharmacology, vol. 123, pp. 19-28.
• Mitchell, J, Whitfield, J, Zhang, W et al 2016, 'Rangefinder: A Semisynthetic FRET Sensor Design Algorithm', ACS Sensors, vol. 1, no. 11, pp. 1286-1290.
• Subramanian, N, Scopelitti, A, Carland, J et al 2016, 'Identification of a 3rd Na+ binding site of the glycine transporter, GlyT2', PLOS ONE (Public Library of Science), vol. 11, no. 6, pp. e0157583-e0157583.
• Subramanian, N, Schumann-Gillett, A, Mark, A et al 2016, 'Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning', Biochimica et Biophysica Acta: Biomembranes, vol. 1858, no. 4, pp. 776-782.
• Ahmed, FH, Mohamed, AE, Carr, P et al 2016, 'Rv2074 is a novel F420H2-dependent biliverdin reductase in Mycobacterium tuberculosis', Protein Science, vol. 25, no. 9, pp. 1692-1709(18).
• Mohamed, AE, Condic-Jurkic, K, Ahmed, H et al 2016, 'Hydrophobic Shielding Drives Catalysis of Hydride Transfer in a Family of F420H2-Dependent Enzymes', Biochemistry, vol. 55, no. 49, pp. 6908-6918pp.
• Subramanian, N, Condic-Jurkic, K & O'Mara, M 2016, 'Structural and dynamic perspectives on the promiscuous transport activity of P-glycoprotein', Neurochemistry International, vol. 98 pp 146-152 doi:10.1016/j.neuint.2016.05.005
• Deplazes, E, Begg, S, van Wonderen, J et al 2015, 'Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy', Biophysical Chemistry, vol. 207, pp. 51-60.
• Fairweather, S, Broer, A, Subramanian, N, Tumer, E, Cheng, Q, Schmoll, D, O'Mara, ML, Bröer, S. 2015, 'Molecular basis for the interaction of the mammalian amino acid transporters B0AT1 and B0AT3 with their ancillary protein collectrin', Journal of Biological Chemistry, vol. 290, no. 40, pp. 24308-24325.
• Brooks, A, Chhabra, Y, Abankwa, D et al 2014, 'S-7: A new cytokine receptor activation paradigm: Activation of JAK2 by the growth hormone receptor', Cytokine, vol. 70, no. 1, pp. 22-22.
• O'Mara, M 2014, 'Joining the Dots Through Molecular Dynamics: Linking the Crystal Structures of a Membrane Transport Protein to its Physiological Conformation', Australian Biochemist, vol. 45, no. 2, pp. 7-11.
• McArthur, J, Singh, G, O'Mara, M et al 2011, 'Orientation of μ-conotoxin PIIIA in a sodium channel vestibule, based on voltage dependence of its binding', Molecular Pharmacology, vol. 80, no. 2, pp. 219-227.
• Crowley, E, O'Mara, M, Kerr, I et al 2010, 'Transmembrane helix 12 plays a pivotal role in coupling energy provision and drug binding in ABCB1', The FEBS Journal, vol. 277, no. 19, pp. 3974-3985.
• Subramanian, N, Condic-Jurkic, K, Mark, AE, O'Mara, ML. 2015, 'Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques', Journal of Chemical Information and Modeling, DOI: 10.1021/ci5007382
• Begg, S, Eijkelkamp, B, Luo, Z et al. 2015, 'Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae', Nature Communications, vol. 6, no. 6418, pp. 1-11.
• Counago, R, Ween, M, Begg, S et al 2014, 'Imperfect coordination chemistry facilitates metal ion release in the psa permease', Nature Chemical Biology, vol. 10, no. 1, pp. 35-U66.
• Plumptre, C, Eijkelkamp, B, Morey, J et al 2014, 'AdcA and AdcAII employ distinct zinc acquisition mechanisms and contribute additively to zinc homeostasis in Streptococcus pneumoniae', Molecular Microbiology, vol. 91, no. 4, pp. 834-851.
• O'Mara, M & Deplazes, E 2014, 'Polypeptide and Protein Modeling for Drug Design', in Dieter Jaeger, Ranu Jung (ed.), Encyclopedia of Computational Neuroscience, Springer New York, New York, NY, pp. 1-9.
• Schmidt, T, O'Mara, M & Kandt, C 2012, 'Molecular Dynamics Simulations of Membrane Proteins: Building Starting Structures and Example Applications', Current Physical Chemistry, vol. 2, no. 4, pp. 363-378.
• Brooks, A, Dai, W, O'Mara, ML et al 2014, 'Mechanism of Activation of Protein Kinase JAK2 by the Growth Hormone Receptor', Science, vol. 344, no. 6185, pp. 1249783
• O'Mara, ML & Mark, AE 2014, 'Structural Characterization of Two Metastable ATP-Bound States of P-Glycoprotein', PLOS ONE (Public Library of Science), vol. 9, no. 3, pp. e91916:1-14.
• van Wonderen, J, McMahon, R, O'Mara, ML et al 2014, 'The central cavity of ABCB1 undergoes alternating access during ATP hydrolysis', The FEBS Journal, vol. 281, no. 9, pp. 2190-2201
• Chen, W, Wang, R, Chen, B et al 2014, 'The ryanodine receptor store-sensing gate controls Ca²⁺ waves and Ca²⁺-triggered arrhythmias', Nature Medicine, vol. 20, no. 2, pp. 184-192.
• Jia, Z, O'Mara, M, Zuegg, J et al 2013, 'Vancomycin: ligand recognition, dimerization and super-complex formation', The FEBS Journal, vol. 280, no. 5, pp. 1294-1307.
• S. L. Neville, J. Sjöhamn, J. A. Watts, H. MacDermott-Opeskin, S. J. Fairweather, K. Ganio, A. C. Hulyer, A. J. Hayes, A. P. McGrath, T. .R. Malcolm, M. R. Davies, N. Nomura, I. So, M. L. O'Mara, C. A. McDevitt and M. J. Maher 2021, 'The structure of the ABC transporter PsaBC shows that bacterial manganese import is achieved by unique architectural features that are conserved across the kingdoms of life', Acta Crystallographica Section A: Foundations and Advances 77(a2):C100-C100.
• O'Mara, M & Mark, A 2012, 'The Effect of Environment on the Structure of a Membrane Protein: P-Glycoprotein under Physiological Conditions', Journal of Chemical Theory and Computation (JCTC), vol. 8, no. 10, pp. 3964-3976.
• Jia, ZG, O'Mara, ML, Zuegg, J et al 2011, 'The Effect of Environment on the Recognition and Binding of Vancomycin to Native and Resistant Forms of Lipid II', Biophysical Journal, vol. 101, pp. 2684-2692.
• Xue, Y, O'Mara, ML, Surawski, P et al 2010, 'Effect of Poly(ethylene glycol) (PEG) Spacers on the Conformational Properties of Small Peptides: A Molecular Dynamics Study', Langmuir, vol. 27, no. 1, pp. 296-303.
• Jones, P, O'Mara, ML & George, A 2009, 'ABC transporters: a riddle wrapped in a mystery inside an enigma', Trends in Biochemical Sciences, vol. 34, no. 10, pp. 520-531.
• Oancea, G, O'Mara, ML, Bennettt, W et al 2009, 'Structural arrangement of the transmission interface in the antigen ABC transport complex TAP', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 14, pp. 5551-5556.
• Procko, E, O'Mara, ML, Bennettt, W et al 2009, 'The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter', The FASEB journal : official publication of the Federation of American Societies for Experimental Biology, vol. 23, pp. 1287-1302.
• Crowley, E, O'Mara, ML, Reynolds, C et al 2009, 'Transmembrane helix 12 modulates progression of the ATP catalytic cycle in ABCB1', Biochemistry, vol. 48, no. 26, pp. 6249-6258.
• Moussatova, A, Kandt, C, O'Mara, ML et al 2008, 'ATP-binding cassette transporters in Eshcerichia coli', Biochimica et Biophysica Acta: Biomembranes, vol. 1778, no. 9, pp. 1757-1771.
• Klassen, T, O'Mara, ML, Redstone, M et al 2008, 'Non-linear intramolecular interactions and voltage sensitivity of a KV1 family potassium channel from Polyorchis penicillatus (Eschscholtz 1829)', Journal of Experimental Biology, vol. 211, pp. 3442-3453.
• O'Mara, ML & Tieleman, DP 2007, 'P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK', FEBS Letters, vol. 581, no. 22, pp. 4217-4222.
• Lawson, J, O'Mara, ML & Kerr, ID 2007, 'Structure-based interpretation of the mutagenesis database for the nucleotide binding domains of P-glycoprotein', Biochimica et Biophysica Acta: Biomembranes, vol. 1778, no. 2, pp. 376-391.
• Storm, J, O'Mara, ML, Crowley, E et al 2007, 'Residue G346 in Transmembrane Segment Six is Involved in Inter-Domain Communication in P-Glycoprotein', Biochemistry, vol. 46, no. 35, pp. 9899-9910.
• O'Mara, ML, Oakley, A & Broer, S 2006, 'Mechanism and Putative Structure of B0-like Neutral Amino Acid Transporters', Journal of Membrane Biology, vol. 213, pp. 111-118.
• Oloo, E, Kandt, C, O'Mara, ML et al 2006, 'Computer simulations of ABC transporter components', Biochemistry and Cell Biology, vol. 84, pp. 900-911.
• O'Mara, ML, Cromer, B, Parker, M et al 2005, 'Homology Model of the GABA_A Receptor Examined Using Brownian Dynamics', Biophysical Journal, vol. 88, pp. 3286-3299.
• Corry, B, O'Mara, M & Chung, S 2004, 'Conduction Mechanisms of Chloride Ions in CIC-Type Channels', Biophysical Journal, vol. 86, pp. 846-860.
• Corry, B, O'Mara, M & Chung, S 2004, 'Permeation Dynamics of Chloride Ions in the CIC-O and CIC-1 Channels', Chemical Physics Letters, vol. 386, pp. 233-238.
• O'Mara, M, Barry, P & Chung, S 2003, 'A Model of the Glycine Receptor Deduced from Brownian Dynamics Studies', PNAS - Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 7, pp. 4310-4315.

Projects and Grants

Grants information is drawn from ARIES. To add or update Projects or Grants information please contact your College Research Office.

• Enzyme-inspired polymer nanomaterials (Secondary Investigator)
• Next generation facility for investigating thermodynamics and kinetics (Secondary Investigator)
• Establishing Nanoscale Design Principles for Nonviral Genome Engineering (Secondary Investigator)
• Glycine Transport Inhibitors for the Treatment of Pain (Secondary Investigator)
• Novel insights into the molecular mechanisms of manganese recognition and acquisition by pathogenic bacteria (Secondary Investigator)
• QUT contracted research: FimH simulations (Primary Investigator)
• Understanding the role of cellular oxidation in AB peptide transport and amyloid formation in pre-clinical Alzheimer's disease using molecular modelling as an alternative to animal studies. (Primary Investigator)
• CBR16/1700032 MD Box: A Cloud based repository and analysis toolkit for molecular dynamics simulations (Secondary Investigator)
• Novel Drugs for the Treatment of Chronic Pain (Secondary Investigator)
• Understanding multidrug resistance: identifying the molecular basis of substrate and inhibitor transport by P-glycoprotein (Primary Investigator)