Megan L. O'Mara

The University of Queensland | UQ

Recent studies have revealed that cancer cell-derived extracellular vesicles (EVs) modulate immunological responses. Lipids have diverse biological functions, and are known to promote tumor malignancy. However, the immunoevasive roles of EV lipids in cancer progression remain poorly understood. Nevertheless, the study of cancer cell-derived EV lipi...

The Gram-negative pathogen Acinetobacter baumannii is a primary contributor to nosocomial multi-drug-resistant (MDR) infections. To combat the rise of MDR infections, novel features of A. baumannii need to be considered for the development of new treatment options. One such feature is the preferential scavenging of exogenous lipids, including host-...

We introduce a single‐chain nanoparticle (SCNP) system capable of catalyzing the photooxidation of nonpolar alkenes up to three times more efficiently than an equivalent small‐molecule photosensitizer at an identical concentration. Specifically, we construct a polymer chain constituted of poly(ethylene glycol) methyl ether methacrylate and glycidyl...

We introduce a single‐chain nanoparticle (SCNP) system capable of catalyzing the photooxidation of nonpolar alkenes up to three times more efficiently than an equivalent small‐molecule photosensitizer at an identical concentration. Specifically, we construct a polymer chain constituted of poly(ethylene glycol) methyl ether methacrylate and glycidyl...

Membrane cholesterol binds to and modulates the function of various SLC6 neurotransmitter transporters, including stabilizing the outward-facing conformation of the dopamine and serotonin transporters. Here, we investigate how cholesterol binds to GlyT2 (SLC6A5), modulates glycine transport rate, and influences bioactive lipid inhibition of GlyT2....

Aryl-urea substituted fatty acids are protonophores and mitochondrial uncouplers that utilise a urea-based synthetic anion transport moiety to carry out the protonophoric cycle. Herein we show that replacement of the urea group with carbamate, a functional group not previously reported to possess anion transport activity, produces analogues that re...

Membrane cholesterol binds to and modulates the function of the specific SLC6 transporters. Here we investigate how cholesterol binds to and modulates the rate of glycine transport by the SLC6 glycine transporter GlyT2, and how this impacts lipid inhibition of GlyT2. Bioactive lipid inhibitors of GlyT2 are analgesics that bind to the lipid alloster...

The binding of the type 1 fimbrial adhesin FimH to mannosylated receptors is allosterically regulated to enhance the fitness of uropathogenic Escherichia coli (UPEC) during urinary tract infection (UTI). Mutations in the two FimH domains (pilin and lectin) located outside the mannose binding pocket have been shown to influence mannose binding affin...

Glycine receptors (GlyRs) containing the α2 subunit govern cell fate, neuronal migration and synaptogenesis in the developing cortex and spinal cord. Rare missense variants and microdeletions in the X-linked GlyR α2 subunit gene (GLRA2) have been associated with human autism spectrum disorder (ASD), where they typically cause a loss-of-function via...

Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using c...

We report the synthesis of two [2]rotaxanes containing an interlocked three dimensional binding cavity formed from a pyridinium bis(amide) axle component containing two phenol donors, and an isophthalamide based macrocycle. In the competitive solvent mixture 1:1 CDCl 3 :CD 3 OD, one of the receptors exhibits a much higher selectivity preference for...

The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential a...

We report the synthesis of two [2]rotaxanes containing an interlocked three dimensional binding cavity formed from a pyridinium bis(amide) axle component containing two phenol donors, and an isophthalamide based macrocycle. In the competitive solvent mixture 1:1 CDCl3:CD3OD, one of the receptors exhibits a much higher selectivity preference for chl...

Heteroleptic [Pd3L2L’3]⁶⁺ cages have been formed from a tritopic ligand (L) and a range of ditopic ligands (L’). Abstract There is a concerted attempt to develop self-assembled metallo-cages of greater structural complexity, and heteroleptic PdII cages are emerging as prime candidates in these efforts. Most of these are dinuclear: few examples of...

Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their po...

Multi-dynamic polymers exhibit improved and unexpected properties compared to materials with only one class of dynamic bond due to co-operative self-assembly. To tune the properties of multi-dynamic materials an understanding...

Inspired by the chemical structure of chymotrypsin, we report an artificial catalytic triad with high catalytic efficiency for the transesterification reaction of vinyl trifluoroacetate and methanol. Rate accelerations of (kcat/kunc)...

The historical sexually transmitted infection gonorrhea continues to be a major public health concern with an estimated global annual incidence of 86.9 million cases. N. gonorrhoeae has been identified by the World Health Organization as one of the 12 antimicrobial-resistant bacterial species that poses the greatest risk to human health. As the maj...

Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. Here, we present the crystal structur...

Antimicrobial resistance is an emerging global health crisis. Consequently, we have a critical need to prolong our current arsenal of antibiotics, in addition to the development of novel treatment options.

At the heart of an enzyme’s structure is the active catalytic site, which, together with the surrounding amino-acid residues, tunes the substrate properties in the electrostatic microenvironment. Taking inspiration from nature’s catalytic triad, consisting of a hydroxyl group of a serine residue, an imidazole group of a histidine residue, and a car...

A coarse-grain model of the epithelial plasma membrane was developed from high-resolution lipidomic data and simulated using the MARTINI force field to characterise its biophysical properties. Plasmalogen lipids, Forssman glycosphingolipids, and hydroxylated Forssman glycosphingolipids and sphingomyelin, were systematically added to determine their...

The local lipid annulus, or “fingerprint”, of four SLC6 transporters (dDAT, hDAT, hSERT, and GlyT2) embedded in a complex neuronal membrane were compared and characterised using molecular dynamics. Our analysis included the development of new tools to improve membrane leaflet detection and the analysis of leaflet-dependent properties. Overall, the...

We use molecular dynamics simulations to characterise the local lipid annulus, or “fingerprint”, of three SLC6 transporters (dDAT, hSERT, and GlyT2) embedded into a complex neuronal membrane. New membrane analysis tools were created to improve leaflet detection and leaflet-dependent properties. Overall, lipid fingerprints are comprised of similar l...

The role of lipids in modulating membrane protein function is an emerging and rapidly growing area of research. The rational design of lipids that target membrane proteins for the treatment of pathological conditions is a novel extension in this field and provides a step forward in our understanding of membrane transporters. Bioactive lipids show c...

The human glycine transporter GlyT2 (SLC6A5) has emerged as a promising drug target for the development of new analgesics to manage chronic pain. N-acyl amino acids inhibit GlyT2 through binding to an allosteric binding site to produce analgesia in vivo with minimal overt side effects. In this paper we use a combination of medicinal chemistry, elec...

Respiring mitochondria establish a proton gradient across the mitochondrial inner membrane (MIM) that is used to generate ATP. Protein-independent mitochondrial uncouplers collapse the proton gradient and disrupt ATP production by shuttling protons back across the MIM in a protonophoric cycle. Continued cycling relies on the formation of MIM-permea...

Cell membranes contain incredible diversity in the chemical structure of their individual lipid species and the ratios in which these lipids are combined to make membranes. Nevertheless, our current understanding of how each of these components effects the properties of the cell membrane remains elusive, in part due to the difficulties in studying...

Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidati...

The remarkable power of enzymes to undertake catalysis frequently stems from their grouping of multiple, complementary chemical units within close proximity around the enzyme active site. Motivated by this, we report here a bioinspired surfactant catalyst that incorporates a variety of chemical functionalities common to hydrolytic enzymes. The text...

The drug efflux pump P-glycoprotein (P-gp) displays a complex transport mechanism involving multiple drug binding sites and two centres for nucleotide hydrolysis. Elucidating the molecular mechanism of transport remains elusive and the availability of P-gp structures in distinct natural and ligand trapped conformations will accelerate our understan...

Divalent metal cations are essential for many biological processes, however accurately modeling divalent metal ions has proved a significant challenge for molecular dynamics forcefields. Here we show that the choice of ion model influences the observed dynamics in PsaA, a metal binding protein from Streptococcus pneumoniae. We conduct extensive unb...

With over 78 million new infections globally each year, gonorrhea remains a frustratingly common infection. Continuous development and spread of antimicrobial-resistant strains of Neisseria gonorrhoeae , the causative agent of gonorrhea, have posed a serious threat to public health. One of the mechanisms in N. gonorrhoeae involved in resistance to...

The treatment of chronic pain is poorly managed by current analgesics, and there is a need for new classes of drugs. We recently developed a series of bioactive lipids that inhibit the human glycine transporter GlyT2 (SLC6A5) and provide analgesia in animal models of pain. Here, we have used functional analysis of mutant transporters combined with...

The recruitment of inhibitory GABA-A receptors to neuronal synapses requires a complex interplay between receptors, neuroligins, the scaffolding protein gephyrin and the GDP-GTP exchange factor collybistin. Collybistin is regulated by protein-protein interactions at the N-terminal SH3 domain, which can bind neuroligins 2/4 and the GABA-AR α2 subuni...

Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools...

The human multidrug transporter P-glycoprotein (P-gp) transports over 200 chemically diverse substrates, influencing their bioavailability and tissue distribution. Pharmacological studies have identified both competitive and non-competitive P-gp substrates, but neither the precise location of the substrate binding sites, nor the basis of competitiv...

The endogenous lipids N-arachidonylglycine and oleoyl-L-carnitine, are potential therapeutic leads in the treatment of chronic pain through their inhibition of the glycine transporter GlyT2. However, their mechanism of action is unknown. It has been hypothesised that these “bioactive” lipids either inhibit GlyT2 indirectly, by significantly perturb...

Oxidation of unsaturated membrane phospholipids by oxidative stress is associated with inflammation, infection, numerous diseases and neurodegenerative disorders. Lipid oxidation is observed in experimental samples when the parent lipid is exposed to oxidative stressors. The effect of phospholipid oxidation on the properties of biological membranes...

SLC6 neurotransmitter transporters facilitate the Na+- and Cl--dependent uptake of amino acids and amino acid derivatives into cells. Disrupting transport leads to a range of neurological disorders. However, the SLC6 substrate transport mechanism is a topic of ongoing debate. Here, we review the prominent SLC6 substrate transport mechanisms through...

Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required...

RMSD time series. The RMSD time series measured for the backbone atoms of (A) the entire protein, (B) transmembrane domain and (C, D) the two nucleotide binding domains for each replica, started from the 3G5U (orange), 4KSB (green) and 4M1M (blue) models. All the protein snapshots were aligned to the relevant domain of the reference structure befor...

P-glycoprotein back view. P-glycoprotein with TMD2 (TM7-12) in front depicted using the 4M1M model. The conserved motifs in the NBDs required for ATP binding and hydrolysis, Walker A and Signature motif (LSSGQ) are highlighted in orange and yellow, respectively. The distance between the Walker A1 (located on NBD1) and the Signature motif on NBD2 is...

Average RMSD. The mean RMSD values and standard deviations were computed for each independent replica, started from 3G5U (orange), 4KSB (green) and 4M1M (blue). The mean RMSD values are given for the entire protein and each domain separately, namely the two nucleotide binding domains (NBD1, NBD2) and the full transmembrane domain (TMD). The TMD* co...

Secondary structure analysis. Secondary structure analysis of TMD1 (TM1-6) and TMD2 (TM7-12) calculated using a simplified version of the DSSP algorithm implemented in the MDTraj package. In the simplified version, only helical (blue), coil (cyan) and strand (yellow) elements are assigned. White vertical lines separate results obtained from each re...

Subspace overlap: 4KSB. Pairwise comparison of the 10 principal components obtained for each simulation based on the 4KSB model (4KSB#1-#3 PCs) and the concatenated (3G5U-4KSB-4M1M) trajectory containing all 9 simulations (cPCs). Subspace overlap was calculated as the root mean squared inner product (RMSIP) of every pair of the principal components...

4KSB #1 trajectory—Front view. The protein movement in the 200 ns trajectory based on the 4KSB model (replica #1). P-glycoprotein is shown in the front view depicting the Λ-conformation with TMD1 in the centre, NBD1 on the right side and NBD2 on the left. Frames shown in the video were taken every 100 ps. Corresponding videos for the replicas 4KSB#...

4M1M #1 trajectory—Side view. The protein movement in the 200 ns trajectory based on the 4M1M model (replica #1). P-glycoprotein is shown in the side view with the TMD1 and NBD1 in front and with the closest lipids (purple) interacting with TM4/TM6 (left) and TM10/TM12 (right) portals. Frames shown in the video were taken every 100 ps. Correspondin...

Principal component variance. Square fluctuations (variances) corresponding to the first 5 principle components (PC1-5) calculated using a concatenated trajectory containing all 9 simulations started from three different crystal structure models (3G5U, 4KSB, 4M1M). The upper panel shows the principal components calculated for the entire protein, wh...

Cholesterol distribution in the 4KSB system. Cholesterol distribution around P-glycoprotein in the simulations based on the 4KSB model at (A) the beginning of the simulations and at 200 ns for each replica: (B) 4KSB #1, (C) 4KSB #2, and (D) 4KSB #3. The cholesterol molecules are shown in dark violet (upper leaflet) and light violet (lower leaflet)...

Cholesterol distribution in the 4M1M system. Cholesterol distribution around P-glycoprotein in the simulations based on the 4M1M model at (A) the beginning of the simulations and at 200 ns for each replica: (B) 4M1M #1, (C) 4M1M #2, and (D) 4M1M #3. The cholesterol molecules are shown in dark violet (upper leaflet) and light violet (lower leaflet)...

Subspace overlap: 3G5U. Pairwise comparison of the 10 principal components obtained for each simulation based on the 3G5U model (3G5U#1-#3 PCs) and the concatenated (3G5U-4KSB-4M1M) trajectory containing all 9 simulations (cPCs). Subspace overlap was calculated as the root mean squared inner product (RMSIP) of every pair of the principal components...

Subspace overlap: 4M1M. Pairwise comparison of the 10 principal components obtained for each simulation based on the 4M1M model (4M1M#1-#3 PCs) and the concatenated (3G5U-4KSB-4M1M) trajectory containing all 9 simulations (cPCs). Subspace overlap was calculated as the root mean squared inner product (RMSIP) of every pair of the principal components...

Covariance overlap. The covariance overlap between each pair of the 9 replicas and the concatenated trajectory calculated for the entire protein and the TMD coordinate subset only. The covariance overlap was calculated as defined in [80] and implemented in the Prody package [75]. This measure asses the similarity of the spaces sampled by two differ...

4KSB #1 trajectory—Side view. The protein movement in the 200 ns trajectory based on the 4KSB model (replica #1). P-glycoprotein is shown in the side view with the TMD1 and NBD1 in front and with the closest lipids (purple) interacting with TM4/TM6 (left) and TM10/TM12 (right) portals. Frames shown in the video were taken every 100 ps. Correspondin...

4M1M #1 trajectory—Front view. The protein movement in the 200 ns trajectory based on the 4M1M model (replica #1). P-glycoprotein is shown in the front view depicting the Λ-conformation with TMD1 in the centre, NBD1 on the right side and NBD2 on the left. Frames shown in the video were taken every 100 ps. Corresponding videos for the replicas 4M1M#...

Domain distances. (A-C) Distances between the Walker A motif (GxxGxGKS) on one NBD and the signature motif (LSGGQ) located on the opposing NBD (shown as d1 and d2 on S1 Fig). (D-F) Distances between NBDs and the intracellular helices at the NBD-TMD interface during triplicate simulations of the 3G5U, 4KSB and 4M1M system. (TIFF)

Cholesterol distribution in the 3G5U system. Cholesterol distribution around P-glycoprotein in the simulations based on the 3G5U model at (A) the beginning of the simulations and at 200 ns for each replica: (B) 3G5U #1, (C) 3G5U #2, and (D) 3G5U #3. The cholesterol molecules are shown in dark violet (upper leaflet) and light violet (lower leaflet)...

3G5U #1 trajectory—Side view. The protein movement in the 200 ns trajectory based on the 3G5U model (replica #1). P-glycoprotein is shown in the side view with the TMD1 and NBD1 in front and with the closest lipids (purple) interacting with TM4/TM6 (left) and TM10/TM12 (right) portals. Frames shown in the video were taken every 100 ps. Correspondin...

Fraction of variance. Fraction of variance corresponding to the first 10 principal components (PC1-10) calculated using each simulation independently (coloured), and a concatenated trajectory containing all 9 simulations started from the three different crystal structure models (black) for (A) the entire protein and (B) only the TMDs. The concatena...

RMSF. Root mean squared fluctuations (RMSF) of Cα atoms in P-gp calculated using data points from three trajectories generated for each system: 3G5U (orange), 4KSB (green) and 4M1M (blue). The upper panel shows the RMSF of Cα atoms of the entire protein, while the lower panel shows RMSF for the TMD only. The highest fluctuations correspond to NBDs...

3G5U #1 trajectory—Front view. The protein movement in the 200 ns trajectory based on the 3G5U model (replica #1). P-glycoprotein is shown in the front view depicting the Λ-conformation with TMD1 in the centre, NBD1 on the right side and NBD2 on the left. Frames shown in the video were taken every 100 ps. Corresponding videos for the replicas 3G5U...

The surface of our planet receives ∼3020 ZJ per year of solar energy annually, which is >5000 times the energy required to power our entire global economy (∼0.6 ZJ per year). Of this energy, ∼43% is photosynthetic active light radiation (PAR) that can be used to drive microalgal biotechnologies for the production of food, fuels, high value products...

Skp and other holdase chaperones bind unfolded bacterial outer membrane proteins, preventing premature folding until they insert into the membrane. In this issue of Structure, Holdbrook et al. (2017) use a combination of NMR, SAXS, ensemble optimization, and MD simulations to show that the Skp chaperone samples a much wider range of conformations t...