Paraskevi Gkeka

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Aminoadamantane derivatives, such as amantadine and rimantadine, have been reported to block the M2 membrane protein of influenza A virus (A/M2TM), but their use has been discontinued due to reported resistance in humans. Understanding the mechanism of action of amantadine derivatives could assist the development of novel potent inhibitors that overcome(More)
We employ coarse-grained molecular dynamics simulations to understand why certain interaction patterns on the surface of a nanoparticle promote its translocation through a lipid membrane. We demonstrate that switching from a random, heterogeneous distribution of hydrophobic and hydrophilic areas on the surface of a nanoparticle to even, homogeneous patterns(More)
The PIK3CA gene is one of the most frequently mutated oncogenes in human cancers. It encodes p110α, the catalytic subunit of phosphatidylinositol 3-kinase alpha (PI3Kα), which activates signaling cascades leading to cell proliferation, survival, and cell growth. The most frequent mutation in PIK3CA is H1047R, which results in enzymatic overactivation.(More)
In this article, we focus on several types of interactions between lipid membranes and alpha-helical peptides, based on the distribution of hydrophobic and hydrophilic residues along the helix. We employ a recently proposed coarse-grained model MARTINI and test its ability to capture diverse types of behavior. MARTINI provides useful insights on the(More)
We perform long-time-scale coarse-grained molecular dynamics simulations of the synthetic amphiphilic LS3 peptide interacting with a DPPC lipid bilayer. Our studies show that within several microseconds, the peptide assembles in a trans-membrane barrel-stave pore. The pore consists of six peptides and has an inner diameter of about 5.2 A, which is(More)
Ligand-functionalized nanoparticles (NPs) are a promising platform for imaging and drug delivery applications. A number of recent molecular simulation and theoretical studies explored how these NPs interact with model lipid membranes. However, interactions between ligand-coated NPs leading to possible cooperative effects and association have not been(More)
Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained(More)
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires(More)
Allosteric modulators offer a novel approach for kinase inhibition because they target less conserved binding sites compared to the active site; thus, higher selectivity may be obtained. PIK-108, a known pan phosphoinositide 3-kinase (PI3K) inhibitor, was recently detected to occupy a non-ATP binding site in the PI3Kα C-lobe. This newly identified pocket is(More)