Structure and Dynamics of Biomembranes containing Cholesterol and other Biologically-Important Sterols : a computational perspective

In this thesis, the differential effects of three closely-related sterols: ergosterol, cholesterol and lanosterol on the structural and dynamical properties of a model dipalmitoyl phosphatidylcholine (DPPC) membrane were examined using Molecular Dynamics (MD) simulations and Neutron Scattering (NS) calculations. As a necessary step towards realistic sterol:biomembrane simulations, molecular mechanics force field parameters for cholesterol, ergosterol and lanosterol, for the program package CHARMM are derived. Subsequently, MD simulations of hydrated sterol:DPPC lipid systems are performed at a biologically-relevant concentration (40\% mol.) at 309K and 323K. The simulations are compared with control simulations of the gel and liquid DPPC phases. All three sterols are found to order and condense the lipids relative to the liquid phase, but to markedly different degrees. Ergosterol is enhancing the packing of the lipids with each other and has a higher condensing effect on the membrane than the other two sterols. Moreover, ergosterol induces a higher proportion of trans lipid conformers, a thicker membrane and higher lipid order parameters, and is aligned more closely with the membrane normal. Ergosterol also positions itself closer to the bilayer:water interface. In contrast, lanosterol orders, straightens and packs the lipids less well, and is less closely aligned with the membrane normal. Furthermore, lanosterol lies closer to the relatively-disordered membrane center than do the other sterols. The behaviour of cholesterol in all the above respects is intermediate between that of lanosterol and ergosterol. The origins of the different membrane behavior upon addition of each sterol are discussed with respect to the sterol chemical differences. Ergosterol was also found to diffuse the slowest and cholesterol the fastest both in the xy-plane and the z-axis of the membrane among the three sterols studied. The findings here may explain why ergosterol is the most efficient of the three sterols at promoting the liquid-ordered phase and lipid domain formation, and may also furnish part of the explanation as to why cholesterol is evolutionarily preferred over lanosterol in higher-vertebrate plasma membranes

\u3cem\u3eIn Vitro\u3c/em\u3e Determination of Potency of Small Molecule Inhibitors of Arp2/3 Complex

Actin is a key protein building block of actin microfilaments, which are constructed and deconstructed in response to cellular signaling pathways to regulate cellular processes such as motility, division, and endocytosis. Arp2/3 Complex is a 7-subunit protein complex that is in involved in cellular construction of branched actin networks, functioning by attaching to the side of a pre-existing actin filament and nucleating a daughter branch. Overexpression of Arp2/3 complex has been linked to the ability of certain metastatic cancers to proliferate. This work describes the synthesis and in vitro biochemical testing of several molecules predicted by computational docking to be inhibitors of Arp2/3 Complex, and therefore of potential interest in clinical applications. A bulk actin polymerization assay is used as the key method to determine the potency of inhibitor candidates. Structure-activity relationships derived from these results are also discussed

Outline Pursuits:Gaze-assisted Selection of Occluded Objects in Virtual Reality

In 3D environments, objects can be difficult to select when they overlap, as this affects available target area and increases selection ambiguity. We introduce Outline Pursuits which extends a primary pointing modality for gaze-assisted selection of occluded objects. Candidate targets within a pointing cone are presented with an outline that is traversed by a moving stimulus. This affords completion of the selection by gaze attention to the intended target's outline motion, detected by matching the user's smooth pursuit eye movement. We demonstrate two techniques implemented based on the concept, one with a controller as the primary pointer, and one in which Outline Pursuits are combined with head pointing for hands-free selection. Compared with conventional raycasting, the techniques require less movement for selection as users do not need to reposition themselves for a better line of sight, and selection time and accuracy are less affected when targets become highly occluded

A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors

Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design

Get a Grip:Evaluating Grip Gestures for VR Input Using a Lightweight Pen

The use of Virtual Reality (VR) in applications such as data analysis, artistic creation, and clinical settings requires high precision input. However, the current design of handheld controllers, where wrist rotation is the primary input approach, does not exploit the human fingers' capability for dexterous movements for high precision pointing and selection. To address this issue, we investigated the characteristics and potential of using a pen as a VR input device. We conducted two studies. The first examined which pen grip allowed the largest range of motion---we found a tripod grip at the rear end of the shaft met this criterion. The second study investigated target selection via 'poking' and ray-casting, where we found the pen grip outperformed the traditional wrist-based input in both cases. Finally, we demonstrate potential applications enabled by VR pen input and grip postures

The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei

Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses. It also possesses two catalytic activities, a tautomerase and an oxidoreductase, though the physiological significance of neither reaction is known. Here, we have determined the crystal structure of MIF from two malaria parasites, Plasmodium falciparum and Plasmodium berghei at 2.2 Å and 1.8 Å, respectively. The structures have an α/β fold and each reveals a trimer, in agreement with the results of analytical ultracentrifugation. We observed open and closed active sites, these being distinguished by movements of proline-1, the catalytic base in the tautomerase reaction. These states correlate with the covalent modification of cysteine 2 to form a mercaptoethanol adduct, an observation confirmed by mass spectrometry. The Plasmodium MIFs have a different pattern of conserved cysteine residues to the mammalian MIFs and the side chain of Cys58, which is implicated in the oxidoreductase activity, is buried. This observation and the evident redox reactivity of Cys2 suggest quite different oxidoreductase characteristics. Finally, we show in pull-down assays that Plasmodium MIF binds to the cell surface receptor CD74, a known mammalian MIF receptor implying that parasite MIF has the ability to interfere with, or modulate, host MIF activity through a competitive binding mechanism

Selective Preservation of Bone Marrow Mature Recirculating but Not Marginal Zone B Cells in Murine Models of Chronic Inflammation

Inflammation promotes granulopoiesis over B lymphopoiesis in the bone marrow (BM). We studied B cell homeostasis in two murine models of T cell mediated chronic inflammation, namely calreticulin-deficient fetal liver chimeras (FLC), which develop severe blepharitis and alopecia due to T cell hyper responsiveness, and inflammatory bowel disease (IBD) caused by injection of CD4+ naïve T cells into lymphopenic mice. We show herein that despite the severe depletion of B cell progenitors during chronic, peripheral T cell-mediated inflammation, the population of BM mature recirculating B cells is unaffected. These B cells are poised to differentiate to plasma cells in response to blood borne pathogens, in an analogous fashion to non-recirculating marginal zone (MZ) B cells in the spleen. MZ B cells nevertheless differentiate more efficiently to plasma cells upon polyclonal stimulation by Toll-like receptor (TLR) ligands, and are depleted during chronic T cell mediated inflammation in vivo. The preservation of mature B cells in the BM is associated with increased concentration of macrophage migration inhibitory factor (MIF) in serum and BM plasma. MIF produced by perivascular dendritic cells (DC) in the BM provides a crucial survival signal for recirculating B cells, and mice treated with a MIF inhibitor during inflammation showed significantly reduced mature B cells in the BM. These data indicate that MIF secretion by perivascular DC may promote the survival of the recirculating B cell pool to ensure responsiveness to blood borne microbes despite loss of the MZ B cell pool that accompanies depressed lymphopoiesis during inflammation

Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics:

The use of antiretrovirals (ARVs) has drastically improved the life quality and expectancy of HIV patients since their introduction in health care. Several millions are still afflicted worldwide by HIV and ARV resistance is a constant concern for both healthcare practitioners and patients, as while treatment options are finite, the virus constantly adapts via complex mutation patterns to select for resistant strains under the pressure of drug treatment. The HIV protease is a crucial enzyme for viral maturation and has been a game changing drug target since the first application. Due to similarities in protease inhibitor designs, drug cross-resistance is not uncommon across ARVs of the same class