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Browsing by Subject "molecular dynamics simulation"

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  • Heinonen, Suvi (2020)
    Diacylglycerol (DAG) is a lipid second messenger, which activates classical and novel protein kinase C (PKC) isozymes at the plasma membrane. Abnormalities in PKC signaling have been linked to several diseases, and defective PKC function connects to multiple pathophysiological components of Alzheimer’s disease. However, aimlessly activating all PKC isozymes with synthetic ligands can be problematic, since the activation of certain isozymes can also promote unwanted processes. There are indications that DAGs with varying degrees of acyl chain saturation may have different and specific PKC activating abilities. Thus, understanding how the structural differences in DAGs relate to their behavior at the lipid bilayer may be beneficial for the development of new, isozyme-specific ligands of PKC. The aim of this master’s thesis was to compare the orientation, positioning and dynamics of two unsaturated DAG molecular species, 1,2-dioleoyl-sn-glycerol (DOG) and 1-stearoyl-2-docosahexaenoyl-sn-glycerol (SDG) in glycerophospholipid bilayers using conventional molecular dynamics (MD) simulations and umbrella sampling. The glycerophospholipid bilayers were composed of either 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE) or 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylethanolamine (SDPE), representing the glycerophospholipid environment in the inner leaflet of the plasma membranes in peripheral tissues and in brain tissue, respectively. Both DAG molecular species displayed very dynamic behavior in all systems, with wide distributions of glycerol moiety tilt angles and acyl chain conformations. Multiple occurrences of transbilayer movement (flip-flop) of DAGs was observed during the MD simulations in all systems. In POPE bilayers, SDG was observed to position closer to the aqueous interface compared to DOG, with larger values of solvent accessible surface area (SASA) of the glycerol moiety and the sn-3 hydroxyl group. In SDPE bilayers, no significant difference in this regard was observed between the DAG molecular species. Although potential of mean force (PMF) profiles did not reveal any major differences in the energetically favoured position of the hydroxyl group between the DAG molecular species, the calculations exposed that the dynamics of DOG are affected more by the surrounding lipid environment compared to SDG. Based on these results, it is probable that while the solvent accessibility and overall position of DAGs is affected by the length and degree of saturation of their acyl chains, there are also other mechanisms and processes causing the differing levels of PKC activation yielded by different DAG molecular species.