Publications

Publication List

A full list of publications from the O’Mara group can be found at Megan’s google scholar page.

2018

  1. A Schumann-Gillett, ML O’Mara. 2018. The effects of oxidised phospholipids and cholesterol on the biophysical properties of POPC bilayers.  Biochimica et Biophysica Acta Biomembranes, doi.org/10.1016/j.bbamem.2018.07.012
  2. A Schumann-Gillett, MT Blyth, ML O’Mara. 2018. Is protein structure enough? A review of the role of lipids in SLC6 transporter function. Neuroscience Letters, doi.org/10.1016/j.neulet.2018.05.020
  3. K Condic-Jurkic, N Subramanian, AE Mark, ML O’Mara. The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment. PLoS One 13:e0191882

2017

  1. J Steinbeck, ML O’Mara, IL Ross, H Stahlberg, B Hankamer. 2017. Thylakoid Ultrastructure: Visualizing the Photosynthetic Machinery. In: Hippler M. (eds) Chlamydomonas: Biotechnology and Biomedicine. Microbiology Monographs, vol 31. Springer, Cham https://doi.org/10.1007/978-3-319-66360-9_7
  2. JE Carland, M Thomas, SN Mostyn, N Subramanian, ML O’Mara, RM Ryan, RJ Vandenberg. 2017. Molecular Determinants for Substrate Interactions with the Glycine Transporter GlyT2. ACS Chemical Neuroscience. 9:603–614.
  3. JA Mitchell, ML O’Mara. 2017. Capturing the Dynamics of a Spring-Loaded Protein. Structure 25:963-64.
  4. A Schumann-Gillett, AE Mark, E Deplazes, ML O’Mara. 2017. A potential new, stable state of the E-cadherin strand-swapped dimer in solution. European Biophysics Journal doi:1007/s00249-017-1229-3
  5. M Thomas, TA Lagones, M Judd, M Morshedi, ML O’Mara, NG White. 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 doi:1002/asia.201700406
  6. MD Nothling, A Ganesan, K Condic-Jurkic, E Pressly, A Davalos, MR Gotrik, Z Xiao, E Khoshdel, CJ Hawker, ML O’Mara, ML Coote, LA Connal. 2017. Simple Design of an Enzyme-Inspired Supported Catalyst Based on a Catalytic Triad. Chem 2:732–745
  7. A Anandan, GL Evans, K Condic-Jurkic, ML O’Mara, CM John, NJ Phillips, GA Jarvis, SS Wills, KA Stubbs, I Moraes, CM Kahler, A Vrielink. 2017. Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding. Proceedings of the National Academy of Sciences USA 114: 2218-2223
  8. JA Kretzmann, D Ho, CW Evans, JHC Plani-Lam, B Garcia-Bloj, AE Mohamed, ML O’Mara, E Ford, DEK Tan, R Lister, P Blancafort, M Norret, KS Iyer. 2017. Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. Chemical Science 8: 2923-2930
  9. JA Mitchell, WH Zhang, MK Herde, C Henneberger, H Janovjak, ML O’Mara, CJ Jackson. 2017. Method for Developing Optical Sensors Using a Synthetic Dye-Fluorescent Protein FRET Pair and Computational Modeling and Assessment. Synthetic Protein Switches: Methods and Protocols, Springer New York, pp 89-99
  10. R Mittra, M Pavy, N Subramanian, AM George, ML O’Mara, ID Kerr, R Callaghan. 2017. Location of contact residues in pharmacologically distinct drug binding sites on P-glycoprotein. Biochemical Pharmacology 123:19-28

2016

  1. AE Mohamed, K Condic-Jurkic, FH Ahmed, P Yuan, ML O’Mara, CJ Jackson, ML Coote. 2016. Hydrophobic Shielding Drives Catalysis of Hydride Transfer in a Family of F420H2-Dependent Enzymes. Biochemistry 55: 6908-6918
  2. JA Mitchell, JH Whitfield, WH Zhang, C Henneberger, H Janovjak, ML O’Mara, CJ Jackson. 2016. Rangefinder: A semi-synthetic FRET sensor design algorithm. ACS Sensors 1:1286-90
  3. Ahmed, FH, AE Mohamed, PD Carr,BM Lee, K Condic-Jurkic, ML O’Mara, CJ Jackson. 2016. Rv2074 is a novel F420H2-dependent biliverdin reductase in Mycobacterium tuberculosis. Protein Science 25:1692-1709
  4. Subramanian, N, AJ Scopelitti, JE Carland, RM Ryan, ML O’Mara, RJ Vandenberg. 2016. Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2. PLoS One 11:e0157583
  5. Subramanian, N, K Condic-Jurkic, ML O’Mara. 2016. Structural and dynamic perspectives on the promiscuous transport activity of P-glycoprotein. Neurochemistry International 98:146-52
  6. Subramanian, N, A Schumann-Gillett, AE Mark, ML O’Mara. Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning. BBA Biomembranes 858:776-782

2015

  1. Deplazes, E, SL Begg, JH van Wonderen, R Campbell, B Kobe, JC Paton, F MacMillan, CA McDevitt, ML O’Mara. 2015. Characterizing the conformational dynamics of metal-free PsaA using molecular dynamics simulations and electron paramagnetic resonance spectroscopy. Biophysical Chemistry 207:51-60
  2. Fairweather, SJ, A Bröer, N Subramanian, E Tumer, Q Cheng, D Schmoll, ML O’ Mara, S Bröer. 2015. Molecular basis for the interaction of the mammalian amino acid transporters B0AT1 and B0AT3 with their ancillary protein collectrin. Journal of Biological Chemistry 290:24308-25
  3. Subramanian, N, K Condic-Jurkic, AE Mark, ML O’Mara. 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 55:1202–1217
  4. Begg, SL, BA Eijkelkamp, Z Luo, RM Couñago, JR Morey, MJ Maher, CY Ong, AG McEwan, B Kobe, ML O’Mara, JC Paton, CA McDevitt. 2015. Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae. Nature Communications, 6:6418

2014

  1. Deplazes, E, and ML O’Mara*. 2014. Polypeptide and Protein Modeling for Drug Design. Encyclopedia of Computational Neuroscience Springer Reference (springerreference.com). Springer-Verlag Berlin Heidelberg. doi:10.1007/SpringerReference_349045 (*corresponding author)
  2. ML O’Mara. Joining the dots through molecular dynamics: linking the crystal structures of a membrane transport protein to its physiological conformation. Australian Biochemist 45:7-11
  3. AJ Brooks, AW Dai, ML O’Mara, D Abankwa, Y Chhabra, RA Pelekanos, O Gardon, KA Tunny, KM Blucher, CJ Morton, MW Parker, E Sierecki, Y Gambin, K Alexandrov, IA Wilson, M Doxastakis, AE Mark, MJ Waters. A new cytokine receptor activation paradigm: activation of JAK2 by the growth hormone receptor. Science 344:1249783
  4. JH van Wonderen*, RM McMahon*, ML O’Mara*, CA McDevitt, AJ Thomson, ID. Kerr, F MacMillan and R Callaghan. 2014. The central cavity of ABCB1 undergoes alternating access during ATP hydrolysis. FEBS Journal, 281: 2190–2201 (*co-first authors)
  5. ML O’Mara* and AE Mark. 2014. Structural characterization of two metastable ATP-bound states of P-glycoprotein. PLoS One 9:e91916 (*corresponding author)
  6. CD Plumptre, BA Eijkelkamp, JR Morey, F Behr, RM Couñago, AD Ogunniyi, B Kobe, ML O’Mara, JC Paton, CA McDevitt. 2014. Zinc homeostasis in Streptococcus pneumoniae and its requirement for bacterial colonization. Molecular Microbiology 91: 834–851
  7. W Chen, R Wang, B Chen, X Zhong, H Kong, Y Bai, Q Zhou, C Xie, J Zhang, A Guo, X Tian, PP Jones, ML O’Mara, Y Liu, T Mi, L Zhang, J Bolstad, L Semeniuk, H Cheng, J Zhang, J Chen, DP Tieleman, AM Gillis, HJ Duff, M Fill, LS Song, SRW Chen. 2014. The Ryanodine Receptor store sensing gate controls Ca2+ waves and Ca2+ triggered arrhythmias. Nature Medicine, 20:184–192

2013

  1. RM Couñago, MP Ween, SL Begg, M Bajaj, J Zuegg, ML O’Mara, MA Cooper, AG McEwan, JC Paton, B Kobe, CA McDevitt. Imperfect coordination chemistry facilitates metal ion release in the Psa permease. Nature Chemical Biology 10:35–41
  2. ZG Jia, ML O’Mara, J Zuegg, MA Cooper and AE Mark. 2013. Vancomycin: ligand recognition, dimerization and super-complex formation. . Journal 280:1294–1307

2012

  1. TH Schmidt, ML O’Mara and C Kandt. 2012. Molecular dynamics simulations of membrane proteins: building starting structures and example applications. Current Physical Chemistry 2: 363-378.
  2. ML O’Mara and AE Mark. 2012. The effect of environment on the structure of a membrane protein: P-glycoprotein under physiological conditions. Journal of Chemical Theory and Computation 8: 3964-3976.
  3. SJ Fairweather, A Broer, ML O’Mara and S Broer. 2012. Intestinal peptidases form functional complexes with neutral amino acid transporter B0AT1 Biochemical Journal 446: 135-148

2011

  1. ZG Jia, ML O’Mara , J Zuegg, MA Cooper and AE Mark. 2011. The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II. Biophysical Journal 101:2684-2692
  2. JR McArthur, G Singh, ML O’Mara, D McMaster, V Ostroumov, DP Tieleman and RJ French. 2011. Orientation of m-conotoxin PIIIA in a sodium channel vestibule, based on its voltage dependence of binding. Molecular Pharmacology 80:219-227
  3. Y Xue*, ML O’Mara*, PPT Surawski, M Trau, and AE Mark. 2011. Effect of Poly(ethylene glycol) (PEG) Spacers on the Conformational Properties of Small Peptides: A Molecular Dynamics Study. Langmuir 27:296-303. (*co-first authors)

2010

  1. E Crowley, ML O’Mara, ID Kerr, R Callaghan. 2010. Transmembrane helix 12 plays a pivotal role in coupling energy provision and drug binding in ABCB1. FEBS Journal 277:3974-85

2009

  1. PM Jones, ML O’Mara, AM George. 2009. ABC transporters: a riddle wrapped in a mystery inside an enigma. Trends in Biochemical Sciences 34:520-31
  2. E Crowley, ML O’Mara, C Reynolds, DP Tieleman, J Storm, ID Kerr, R Callaghan. 2009. Transmembrane Helix 12 Modulate Progression of the ATP Catalytic Cycle in ABCB1. Biochemistry 48:6249-58
  3. E Procko, ML O’Mara, WFD Bennett, DP Tieleman and R Gaudet. 2009. The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter. FASEB Journal 23:1287-1302
  4. G Oancea, ML O’Mara, WFD Bennett, DP Tieleman, R Abele and R Tampé. 2009. Structural Arrangement of the Transmission Interface in the ABC Transporter TAP Critical for Antigen Binding and Translocation. Proceedings of the National Academy of Sciences 106:5551-56

2008

  1. TL Klassen, ML O’Mara, M Redstone, AN Spencer, WJ Gallin. 2008. Non-linear intramolecular interactions and voltage sensitivity of a K V1 family potassium channel from Polyorchis penicillatus (Eschscholtz 1829) Journal of Experimental Biology 211:3442-53
  2. A Moussatova, C Kandt, ML O’Mara, DP Tieleman. 2008. ATP binding cassette transporters in Escherichia coli. BBA Biomembranes 1778:1757-71
  3. J Storm, S Modok, ML O’Mara, DP Tieleman, ID Kerr, R Callaghan. 2008. The cytosolic region of TM6 in P-glycoprotein: topographical analysis and functional perturbation by site directed labelling. Biochemistry 47:3615-24

2007

  1. J Lawson, ML O’Mara, ID Kerr. 2007. Structure-based interpretation of the mutagenesis database for the nucleotide binding domains of P-glycoprotein. BBA Biomembranes 1778:376-91
  2. ML O’Mara and DP Tieleman. 2007. P-glycoprotein models of apo and ATP-bound states based on homology with Sav1866 and MalK. FEBS Letters 581:4217-22
  3. J Storm, ML O’Mara, E Crowley, J Peall, DP Tieleman, ID Kerr and R Callaghan. 2007. Residue G346C in the transmembrane segment six is involved in inter-domain communication in P-glycoprotein. Biochemistry 46:9899-9910

2006

  1. E Oloo, C Kandt, ML O’Mara and DP Tieleman. 2006. Computer simulations of ABC transporter components. Biochemistry and Cell Biology 84:900-911
  2. ML O’Mara, A Oakley and S Broer. 2006. Mechanism and putative structure of B0-like neutral amino acid transporters. Journal of Membrane Biology 213:111-18

2005

  1. ML O’Mara, BA Cromer, MW Parker and SH Chung. 2005. Homology Model of the GABAA Receptor Examined Using Brownian Dynamics. Biophysical Journal 88:3286-99

2004

  1. B Corry, M O’Mara and SH Chung. 2004. Permeation dynamics of chloride ions in the ClC-0 and ClC-1 channels. Chemical Physics Letters 386:233-238
  2. B Corry, M O’Mara and SH Chung, 2004. Conduction Mechanisms of Chloride Ions in ClC-type Channels. Biophysical Journal 86:846-60

2003

  1. M O’Mara, PH Barry and SH Chung. 2003. A model of the glycine receptor deduced from Brownian dynamics studies. Proceedings of the National Academy of Sciences USA 100:4310-15
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