ABSTRACT The first step into assessing the nanoparticle (NP) cytotoxicity requires a thorough und... more ABSTRACT The first step into assessing the nanoparticle (NP) cytotoxicity requires a thorough understanding of the NP-membrane interaction mechanism. The main aim of this study is to investigate the relationship of the surface hydrophobicity distribution of the NP with its translocation efficiency. Two types of NPs, one with a random and one with a striped hydrophobic-hydrophilic surface pattern, are investigated using Molecular Dynamics (MD) simulations and free-energy calculations. The MARTINI coarse-grained description is employed. The results illustrate the significance of the NP surface chemistry pattern by revealing that an ordered distribution of surface hydrophilic groups gives rise to generically different behavior to that of a NP with randomly placed surface hydrophilic groups. The stripedpatterned NP prefers to adopt an interfacial positioning on the membrane, whereas the random-patterned NP gets ` trapped' within the lipid bilayer. From an inverse engineering point of view, the present study provides insight into the surface design of NPs with tailored functionalities, such as direct cellular entry and maximization of cellular uptake.
Peptide-membrane interactions play an important role in a number of biological processes, such as... more Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions of membrane proteins. In particular, amphipathic α-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic α-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endoand pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and the mechanism of interaction it induces, as well as molecular details of this process, still remain elusive. Lack of this knowledg...
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells.... 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 knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
The journal of physical chemistry. B, Jan 22, 2015
Allosteric modulators offer a novel approach for kinase inhibition because they target less conse... 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 located close to residue 1047, which is frequently mutated in human cancers (H1047R). In order to assess the interactions, stability, and any possible allosteric effects of this inhibitor on PI3Kα, extensive molecular dynamics (MD) simulations in aqueous solution were performed for the wild type (WT) human, WT murine, and H1047R human mutant PI3Kα proteins with PIK-108 placed in both catalytic and non-ATP sites. We verify the existence of the second binding site in the vicinity of the hotspot H1047R PI3Kα mutation through binding site identification and MD simulations. PIK-108 remains stable in both sites in all three variants th...
We employ coarse-grained molecular dynamics simulations to understand why certain interaction pat... 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 substantially flattens the translocation free-energy profile and dramatically enhances permeation. We then proceed to construct a more detailed coarse-grained model of a nanoparticle with flexible hydrophobic and hydrophilic ligands arranged into striped domains. Molecular dynamics simulations of these nanoparticles show that the terminal groups of the ligands tend to arrange themselves into homogeneous patterns, despite the underlying striped domains. These observations are linked to recent experimental studies.
Aminoadamantane derivatives, such as amantadine and rimantadine, have been reported to block the ... more 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 A/M2TM resistance. Here, we use Free Energy Perturbation calculations coupled with Molecular Dynamics simulations (FEP/MD) to rationalize the thermodynamic origin of binding preference of several aminoadamantane derivatives inside the A/M2TM pore. Our results demonstrate that apart from crucial protein-ligand intermolecular interactions, the flexibility of the protein, the water network around the ligand, and the desolvation free energy penalty to transfer the ligand from the aqueous environment to the transmembrane region are key elements for the binding preference of these compounds and thus for lead optimization. The high correlation of the FEP/MD results with available experimental data (R(2) = 0.85) demonstrates that this methodology holds predictive value and can be used to guide the optimization of drug candidates binding to membrane proteins.
Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretchi... 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 Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the...
ABSTRACT The first step into assessing the nanoparticle (NP) cytotoxicity requires a thorough und... more ABSTRACT The first step into assessing the nanoparticle (NP) cytotoxicity requires a thorough understanding of the NP-membrane interaction mechanism. The main aim of this study is to investigate the relationship of the surface hydrophobicity distribution of the NP with its translocation efficiency. Two types of NPs, one with a random and one with a striped hydrophobic-hydrophilic surface pattern, are investigated using Molecular Dynamics (MD) simulations and free-energy calculations. The MARTINI coarse-grained description is employed. The results illustrate the significance of the NP surface chemistry pattern by revealing that an ordered distribution of surface hydrophilic groups gives rise to generically different behavior to that of a NP with randomly placed surface hydrophilic groups. The stripedpatterned NP prefers to adopt an interfacial positioning on the membrane, whereas the random-patterned NP gets ` trapped' within the lipid bilayer. From an inverse engineering point of view, the present study provides insight into the surface design of NPs with tailored functionalities, such as direct cellular entry and maximization of cellular uptake.
Peptide-membrane interactions play an important role in a number of biological processes, such as... more Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions of membrane proteins. In particular, amphipathic α-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic α-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endoand pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and the mechanism of interaction it induces, as well as molecular details of this process, still remain elusive. Lack of this knowledg...
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells.... 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 knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
The journal of physical chemistry. B, Jan 22, 2015
Allosteric modulators offer a novel approach for kinase inhibition because they target less conse... 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 located close to residue 1047, which is frequently mutated in human cancers (H1047R). In order to assess the interactions, stability, and any possible allosteric effects of this inhibitor on PI3Kα, extensive molecular dynamics (MD) simulations in aqueous solution were performed for the wild type (WT) human, WT murine, and H1047R human mutant PI3Kα proteins with PIK-108 placed in both catalytic and non-ATP sites. We verify the existence of the second binding site in the vicinity of the hotspot H1047R PI3Kα mutation through binding site identification and MD simulations. PIK-108 remains stable in both sites in all three variants th...
We employ coarse-grained molecular dynamics simulations to understand why certain interaction pat... 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 substantially flattens the translocation free-energy profile and dramatically enhances permeation. We then proceed to construct a more detailed coarse-grained model of a nanoparticle with flexible hydrophobic and hydrophilic ligands arranged into striped domains. Molecular dynamics simulations of these nanoparticles show that the terminal groups of the ligands tend to arrange themselves into homogeneous patterns, despite the underlying striped domains. These observations are linked to recent experimental studies.
Aminoadamantane derivatives, such as amantadine and rimantadine, have been reported to block the ... more 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 A/M2TM resistance. Here, we use Free Energy Perturbation calculations coupled with Molecular Dynamics simulations (FEP/MD) to rationalize the thermodynamic origin of binding preference of several aminoadamantane derivatives inside the A/M2TM pore. Our results demonstrate that apart from crucial protein-ligand intermolecular interactions, the flexibility of the protein, the water network around the ligand, and the desolvation free energy penalty to transfer the ligand from the aqueous environment to the transmembrane region are key elements for the binding preference of these compounds and thus for lead optimization. The high correlation of the FEP/MD results with available experimental data (R(2) = 0.85) demonstrates that this methodology holds predictive value and can be used to guide the optimization of drug candidates binding to membrane proteins.
Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretchi... 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 Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the...
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Papers by Evi Gkeka