15 research outputs found
C<sub>3</sub> stereoisomer of tris-malonic fullerene.
<p>A. Free energy profile of the process of the C<sub>3</sub> penetration into the model eukaryotic membrane. B. Intermediate orientation of the C<sub>3</sub> molecule adsorbed to the membrane with its solvent shell retained. C. Stable conformation (corresponding to the global energy minimum of the free energy profile) of C<sub>3</sub> adsorbed to the membrane and established hydrophobic contact with the lipid tails region.</p
D<sub>3</sub> stereoisomer of tris-malonic fullereneB
<p>A. Free energy profile of the process of the D<sub>3</sub> penetration into the model eukaryotic membrane. B. Orientation (corresponding to the global energy minimum of the free energy profile) of the D<sub>3</sub> molecule adsorbed to the membrane.</p
Properties of the DPPC membrane in simulations with different amount of fullerenes.
<p>Properties of the DPPC membrane in simulations with different amount of fullerenes.</p
Comparison of available computational studies of the interaction of C<sub>60</sub> with lipid bilayer.
<p>Comparison of available computational studies of the interaction of C<sub>60</sub> with lipid bilayer.</p
Comparative Computational Study of Interaction of C<sub>60</sub>-Fullerene and Tris-Malonyl-C<sub>60</sub>-Fullerene Isomers with Lipid Bilayer: Relation to Their Antioxidant Effect
<div><p>Oxidative stress induced by excessive production of reactive oxygen species (ROS) has been implicated in the etiology of many human diseases. It has been reported that fullerenes and some of their derivatives–carboxyfullerenes–exhibits a strong free radical scavenging capacity. The permeation of C<sub>60</sub>-fullerene and its amphiphilic derivatives–C<sub>3</sub>-tris-malonic-C<sub>60</sub>-fullerene (C<sub>3</sub>) and D<sub>3</sub>-tris-malonyl-C<sub>60</sub>-fullerene (D<sub>3</sub>)–through a lipid bilayer mimicking the eukaryotic cell membrane was studied using molecular dynamics (MD) simulations. The free energy profiles along the normal to the bilayer composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) for C<sub>60</sub>, C<sub>3</sub> and D<sub>3</sub> were calculated. We found that C<sub>60</sub> molecules alone or in clusters spontaneously translocate to the hydrophobic core of the membrane and stay inside the bilayer during the whole period of simulation time. The incorporation of cluster of fullerenes inside the bilayer changes properties of the bilayer and leads to its deformation. In simulations of the tris-malonic fullerenes we discovered that both isomers, C<sub>3</sub> and D<sub>3</sub>, adsorb at the surface of the bilayer but only C<sub>3</sub> tends to be buried in the area of the lipid headgroups forming hydrophobic contacts with the lipid tails. We hypothesize that such position has implications for ROS scavenging mechanism in the specific cell compartments.</p></div
Characteristics of fullerene-membrane interactions.
<p>A. Distance between the center of mass (COM) of C<sub>60</sub> and COM of the membrane. On the third nanosecond fullerene spontaneously “jump” into the membrane (the membrane surface is shown with the dot line). B. Free energy profile of the process of the C<sub>60</sub> penetration into the model eukaryotic membrane. Potential wall at 30 Å is shown as the dotted line. C. Snapshot of the system with a single C<sub>60</sub> molecule inside the membrane.</p
Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations
Phthalocyanines
are aromatic macrocyclic compounds, which are structurally
related to porphyrins. In clinical practice, phthalocyanines are used
in fluorescence imaging and photodynamic therapy of cancer and noncancer
lesions. Certain forms of the substituted polycationic metallophthalocyanines
have been previously shown to be active in photodynamic inactivation
of both Gram-negative and Gram-positive bacteria; one of them is zinc
octakisÂ(cholinyl)Âphthalocyanine (ZnPcChol<sup>8+</sup>). However,
the molecular details of how these compounds translocate across bacterial
membranes still remain unclear. In the present work, we have developed
a coarse-grained (CG) molecular model of ZnPcChol<sup>8+</sup> within
the framework of the popular MARTINI CG force field. The obtained
model was used to probe the solvation behavior of phthalocyanine molecules,
which agreed with experimental results. Subsequently, it was used
to investigate the molecular details of interactions between phthalocyanines
and membranes of various compositions. The results demonstrate that
ZnPcChol<sup>8+</sup> has high affinity to both the inner and the
outer model membranes of Gram-negative bacteria, although this species
does not show noticeable affinity to the 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphatidylcholine membrane. Furthermore,
we found out that the process of ZnPcChol<sup>8+</sup> penetration
toward the center of the outer bacterial membrane is energetically
favorable and leads to its overall disturbance and formation of the
aqueous pore. Such intramembrane localization of ZnPcChol<sup>8+</sup> suggests their twofold cytotoxic effect on bacterial cells: (1)
via induction of lipid peroxidation by enhanced production of reactive
oxygen species (i.e., photodynamic toxicity); (2) via rendering the
bacterial membrane more permeable for additional Pc molecules as well
as other compounds. We also found that the kinetics of penetration
depends on the presence of phospholipid defects in the lipopolysaccharide
leaflet of the outer membrane and the type of counterions, which stabilize
it. Thus, the results of our simulations provide a detailed molecular
view of ZnPcChol<sup>8+</sup> “self-promoted uptake”,
the pathway previously proposed for some small molecules crossing
the outer bacterial membrane
Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of <i>Natronomonas pharaonis</i>
<div><p>Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely <i>Np</i>SRII/<i>Np</i>HtrII from <i>Natronomonas pharaonis</i>. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of <i>Np</i>SRII/<i>Np</i>HtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for <i>E</i>. <i>coli</i> chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors.</p></div
Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations
Phthalocyanines
are aromatic macrocyclic compounds, which are structurally
related to porphyrins. In clinical practice, phthalocyanines are used
in fluorescence imaging and photodynamic therapy of cancer and noncancer
lesions. Certain forms of the substituted polycationic metallophthalocyanines
have been previously shown to be active in photodynamic inactivation
of both Gram-negative and Gram-positive bacteria; one of them is zinc
octakisÂ(cholinyl)Âphthalocyanine (ZnPcChol<sup>8+</sup>). However,
the molecular details of how these compounds translocate across bacterial
membranes still remain unclear. In the present work, we have developed
a coarse-grained (CG) molecular model of ZnPcChol<sup>8+</sup> within
the framework of the popular MARTINI CG force field. The obtained
model was used to probe the solvation behavior of phthalocyanine molecules,
which agreed with experimental results. Subsequently, it was used
to investigate the molecular details of interactions between phthalocyanines
and membranes of various compositions. The results demonstrate that
ZnPcChol<sup>8+</sup> has high affinity to both the inner and the
outer model membranes of Gram-negative bacteria, although this species
does not show noticeable affinity to the 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphatidylcholine membrane. Furthermore,
we found out that the process of ZnPcChol<sup>8+</sup> penetration
toward the center of the outer bacterial membrane is energetically
favorable and leads to its overall disturbance and formation of the
aqueous pore. Such intramembrane localization of ZnPcChol<sup>8+</sup> suggests their twofold cytotoxic effect on bacterial cells: (1)
via induction of lipid peroxidation by enhanced production of reactive
oxygen species (i.e., photodynamic toxicity); (2) via rendering the
bacterial membrane more permeable for additional Pc molecules as well
as other compounds. We also found that the kinetics of penetration
depends on the presence of phospholipid defects in the lipopolysaccharide
leaflet of the outer membrane and the type of counterions, which stabilize
it. Thus, the results of our simulations provide a detailed molecular
view of ZnPcChol<sup>8+</sup> “self-promoted uptake”,
the pathway previously proposed for some small molecules crossing
the outer bacterial membrane
Inter-dimeric distances for related residues of the transducer.
<p>Distances were calculated as an average over the three dimers for the methylated (black) and demethylated (red) states, shaded areas representing the standard deviation. The distance is measured between the center of mass (COM) of two related residues in one dimer and the COM of the six respective residues in the trimer-of-dimers (see inset on the lower left). The domains of the complex are depicted in colored bars; m.s and A/W indicate methylation sites and binding sites for CheA/CheW, respectively. Representative distance trajectories are depicted in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004561#pcbi.1004561.s007" target="_blank">S7 Fig</a>.</p