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Félix S. Csajka - One of the best experts on this subject based on the ideXlab platform.

  • Transition path sampling study of flip-flop transitions in Model Lipid Bilayer membranes.
    Physical review. E Statistical nonlinear and soft matter physics, 2004
    Co-Authors: Jordi Martí, Félix S. Csajka
    Abstract:

    The microscopic dynamics of Lipids in biomembranes is of special relevance in the study of chemical reactions produced in cells. The mechanism of the exchange of a Model Lipid molecule between both sides of a flexible Bilayer membrane or flip-flop in an aqueous environment has been studied by computer simulation using the recently developed transition path sampling technique, since flip-flop transitions are infrequent events of the Lipid dynamics. In addition, structural changes in the membrane have been investigated at ambient conditions and for increasing temperature. Our results highlight the cooperative effort of the whole system in order to allow a Lipid molecule to cross the bottleneck in configuration space associated with the transition state of the flip-flop event. Within the time interval of the transition, all molecules of the system significantly change the frequency of their molecular motions.

  • Flip-flop dynamics in a Model Lipid Bilayer membrane
    Europhysics Letters (EPL), 2003
    Co-Authors: Jordi Martí, Félix S. Csajka
    Abstract:

    The transition states associated to the dynamics of a Model Lipid Bilayer membrane have been investigated by means of molecular-dynamics transition path sampling. We have focused on the flip-flop transition of a Lipid molecule between the two sides of a flexible membrane. In the transition state, a local collective reorganization is necessary to allow a Lipid molecule to move from one interface of the Bilayer to the second one. The elapsed time for flip-flop has been estimated to be 0.27 ps, whereas the increase in configurational energy during the flip-flop transition is of about 15 kJ/mol.

Tian-xiang Xiang - One of the best experts on this subject based on the ideXlab platform.

  • MEAN MOLECULAR POTENTIALS IN A Model Lipid Bilayer: A MOLECULAR DYNAMICS SIMULATION
    The Journal of Chemical Physics, 1995
    Co-Authors: Tian-xiang Xiang, Bradley D Anderson
    Abstract:

    Various mean‐field potentials in a Model Lipid Bilayer are calculated by means of molecular dynamics (MD) simulation. The Bilayer assembly consists of 200 chain molecules. The anisotropic united atom Model is employed for nonbonded interactions and is extended to allow bond length to vary with time. The interfacial translational order is systematically varied and found to correlate strongly with the chain orientational order. A new torsional potential is developed and shown to give order parameters in better agreement with experiment than the Padilla–Toxvaerd potential. Nonbonded interaction reduces the trans–gauche and gauche–gauche transition barriers by 0.9—1.5 kcal/mole. The mean trans–gauche energy difference near the chain tail is close to that in liquid hydrocarbons but 0.34 kcal/mol lower than that in the highly ordered chain region. In contrast to the Marcelja Model, both mean intermolecular dispersive and repulsive energies depend exponentially on the chain orientational parameter and the repuls...

  • Molecular distributions in interphases: statistical mechanical theory combined with molecular dynamics simulation of a Model Lipid Bilayer
    Biophysical Journal, 1994
    Co-Authors: Tian-xiang Xiang, Bradley D Anderson
    Abstract:

    A mean-field statistical mechanical theory has been developed to describe molecular distributions in interphases. The excluded volume interaction has been Modeled in terms of a reversible work that is required to create a cavity of the solute size against a pressure tensor exerted by the surrounding interphase molecules. The free energy change associated with this compression process includes the configuration entropy as well as the change in conformational energy of the surrounding chain molecules. The lateral pressure profile in a Model Lipid Bilayer (30.5 A2/chain molecule) has been calculated as a function of depth in the Bilayer interior by molecular dynamics simulation. The lateral pressure has a plateau value of 309 +/- 48 bar in the highly ordered region and decreases abruptly in the center of the Bilayer. Model calculations have shown that for solute molecules with ellipsoidal symmetry, the orientational order increases with the ratio of the long to short molecular axes at a given solute volume and increases with solute volume at a given axial ratio, in accordance with recent experimental data. Increased lateral pressure (p perpendicular) results in higher local order and exclusion of solute from the interphase, in parallel with the effect of surface density on the partitioning and local order. The logarithm of the interphase/water partition coefficient for spherical solutes decreases linearly with solute volume. This is also an excellent approximation for elongated solutes because of the relatively weak dependence of solute partitioning on molecular shape. The slope is equal to (2p perpendicular - p parallel)/3KBT, where p parallel is the normal pressure component, and different from that predicted by the mean-field lattice theory. Finally, the lattice theory has been extended herein to incorporate an additional constraint on chain packing in the interphase and to account for the effect of solute size on partitioning.

  • A computer simulation of free-volume distributions and related structural properties in a Model Lipid Bilayer.
    Biophysical journal, 1993
    Co-Authors: Tian-xiang Xiang
    Abstract:

    A novel combined approach of molecular dynamics (MD) and Monte Carlo simulations is developed to calculate various free-volume distributions as a function of position in a Lipid Bilayer membrane at 323 K. The Model Bilayer consists of 2 x 100 chain molecules with each chain molecule having 15 carbon segments and one head group and subject to forces restricting bond stretching, bending, and torsional motions. At a surface density of 30 A2/chain molecule, the probability density of finding effective free volume available to spherical permeants displays a distribution with two exponential components. Both pre-exponential factors, p1 and p2, remain roughly constant in the highly ordered chain region with average values of 0.012 and 0.00039 A-3, respectively, and increase to 0.049 and 0.0067 A-3 at the mid-plane. The first characteristic cavity size V1 is only weakly dependent on position in the Bilayer interior with an average value of 3.4 A3, while the second characteristic cavity size V2 varies more dramatically from a plateau value of 12.9 A3 in the highly ordered chain region to 9.0 A3 in the center of the Bilayer. The mean cavity shape is described in terms of a probability distribution for the angle at which the test permeant is in contact with one of and does not overlap with anyone of the chain segments in the Bilayer. The results show that (a) free volume is elongated in the highly ordered chain region with its long axis normal to the Bilayer interface approaching spherical symmetry in the center of the Bilayer and (b) small free volume is more elongated than large free volume. The order and conformational structures relevant to the free-volume distributions are also examined. It is found that both overall and internal motions have comparable contributions to local disorder and couple strongly with each other, and the occurrence of kink defects has higher probability than predicted from an independent-transition Model.

Bradley D Anderson - One of the best experts on this subject based on the ideXlab platform.

  • MEAN MOLECULAR POTENTIALS IN A Model Lipid Bilayer: A MOLECULAR DYNAMICS SIMULATION
    The Journal of Chemical Physics, 1995
    Co-Authors: Tian-xiang Xiang, Bradley D Anderson
    Abstract:

    Various mean‐field potentials in a Model Lipid Bilayer are calculated by means of molecular dynamics (MD) simulation. The Bilayer assembly consists of 200 chain molecules. The anisotropic united atom Model is employed for nonbonded interactions and is extended to allow bond length to vary with time. The interfacial translational order is systematically varied and found to correlate strongly with the chain orientational order. A new torsional potential is developed and shown to give order parameters in better agreement with experiment than the Padilla–Toxvaerd potential. Nonbonded interaction reduces the trans–gauche and gauche–gauche transition barriers by 0.9—1.5 kcal/mole. The mean trans–gauche energy difference near the chain tail is close to that in liquid hydrocarbons but 0.34 kcal/mol lower than that in the highly ordered chain region. In contrast to the Marcelja Model, both mean intermolecular dispersive and repulsive energies depend exponentially on the chain orientational parameter and the repuls...

  • Molecular distributions in interphases: statistical mechanical theory combined with molecular dynamics simulation of a Model Lipid Bilayer
    Biophysical Journal, 1994
    Co-Authors: Tian-xiang Xiang, Bradley D Anderson
    Abstract:

    A mean-field statistical mechanical theory has been developed to describe molecular distributions in interphases. The excluded volume interaction has been Modeled in terms of a reversible work that is required to create a cavity of the solute size against a pressure tensor exerted by the surrounding interphase molecules. The free energy change associated with this compression process includes the configuration entropy as well as the change in conformational energy of the surrounding chain molecules. The lateral pressure profile in a Model Lipid Bilayer (30.5 A2/chain molecule) has been calculated as a function of depth in the Bilayer interior by molecular dynamics simulation. The lateral pressure has a plateau value of 309 +/- 48 bar in the highly ordered region and decreases abruptly in the center of the Bilayer. Model calculations have shown that for solute molecules with ellipsoidal symmetry, the orientational order increases with the ratio of the long to short molecular axes at a given solute volume and increases with solute volume at a given axial ratio, in accordance with recent experimental data. Increased lateral pressure (p perpendicular) results in higher local order and exclusion of solute from the interphase, in parallel with the effect of surface density on the partitioning and local order. The logarithm of the interphase/water partition coefficient for spherical solutes decreases linearly with solute volume. This is also an excellent approximation for elongated solutes because of the relatively weak dependence of solute partitioning on molecular shape. The slope is equal to (2p perpendicular - p parallel)/3KBT, where p parallel is the normal pressure component, and different from that predicted by the mean-field lattice theory. Finally, the lattice theory has been extended herein to incorporate an additional constraint on chain packing in the interphase and to account for the effect of solute size on partitioning.

Jordi Martí - One of the best experts on this subject based on the ideXlab platform.

  • A molecular dynamics transition path sampling study of Model Lipid Bilayer membranes in aqueous environments
    Journal of Physics: Condensed Matter, 2004
    Co-Authors: Jordi Martí
    Abstract:

    The transversal motion of Lipids across biological membranes or flip–flop in aqueous media is of fundamental importance in understanding chemical reactions produced in cells. It is also an example of a rare event in a biological system. Such a process has been investigated by molecular dynamics transition path sampling, which is a powerful tool designed to deal with rare events in a wide range of systems. The study covers a wide range of temperature conditions and includes the analysis of flip–flop free energies together with a detailed study of vibrational densities of states associated with flip–flop motions.

  • Transition path sampling study of flip-flop transitions in Model Lipid Bilayer membranes.
    Physical review. E Statistical nonlinear and soft matter physics, 2004
    Co-Authors: Jordi Martí, Félix S. Csajka
    Abstract:

    The microscopic dynamics of Lipids in biomembranes is of special relevance in the study of chemical reactions produced in cells. The mechanism of the exchange of a Model Lipid molecule between both sides of a flexible Bilayer membrane or flip-flop in an aqueous environment has been studied by computer simulation using the recently developed transition path sampling technique, since flip-flop transitions are infrequent events of the Lipid dynamics. In addition, structural changes in the membrane have been investigated at ambient conditions and for increasing temperature. Our results highlight the cooperative effort of the whole system in order to allow a Lipid molecule to cross the bottleneck in configuration space associated with the transition state of the flip-flop event. Within the time interval of the transition, all molecules of the system significantly change the frequency of their molecular motions.

  • Flip-flop dynamics in a Model Lipid Bilayer membrane
    Europhysics Letters (EPL), 2003
    Co-Authors: Jordi Martí, Félix S. Csajka
    Abstract:

    The transition states associated to the dynamics of a Model Lipid Bilayer membrane have been investigated by means of molecular-dynamics transition path sampling. We have focused on the flip-flop transition of a Lipid molecule between the two sides of a flexible membrane. In the transition state, a local collective reorganization is necessary to allow a Lipid molecule to move from one interface of the Bilayer to the second one. The elapsed time for flip-flop has been estimated to be 0.27 ps, whereas the increase in configurational energy during the flip-flop transition is of about 15 kJ/mol.

W. Yap - One of the best experts on this subject based on the ideXlab platform.

  • supported phosphoLipid alkanethiol biomimetic membranes insulating properties
    Biophysical Journal, 1994
    Co-Authors: Anne L. Plant, M. Gueguetchkeri, W. Yap
    Abstract:

    A novel Model Lipid Bilayer membrane is prepared by the addition of phosphoLipid vesicles to alkanethiol monolayers on gold. This supported hybrid Bilayer membrane is rugged, easily and reproducibly prepared in the absence of organic solvent, and is stable for very long periods of time. We have characterized the insulating characteristics of this membrane by examining the rate of electron transfer and by impedance spectroscopy. Supported hybrid Bilayers formed from phosphoLipids and alkanethiols are pinhole-free and demonstrate measured values of conductivity and resistivity which are within an order of magnitude of that reported for black Lipid membranes. Capacitance values suggest a dielectric constant of 2.7 for phosphoLipid membranes in the absence of organic solvent. The protein toxin, melittin, destroys the insulating capability of the phosphoLipid layer without significantly altering the Bilayer structure. This Model membrane will allow the assessment of the effect of Lipid membrane perturbants on the insulating properties of natural Lipid membranes.

  • Supported phosphoLipid/alkanethiol biomimetic membranes: insulating properties
    Biophysical journal, 1994
    Co-Authors: Anne L. Plant, M. Gueguetchkeri, W. Yap
    Abstract:

    A novel Model Lipid Bilayer membrane is prepared by the addition of phosphoLipid vesicles to alkanethiol monolayers on gold. This supported hybrid Bilayer membrane is rugged, easily and reproducibly prepared in the absence of organic solvent, and is stable for very long periods of time. We have characterized the insulating characteristics of this membrane by examining the rate of electron transfer and by impedance spectroscopy. Supported hybrid Bilayers formed from phosphoLipids and alkanethiols are pinhole-free and demonstrate measured values of conductivity and resistivity which are within an order of magnitude of that reported for black Lipid membranes. Capacitance values suggest a dielectric constant of 2.7 for phosphoLipid membranes in the absence of organic solvent. The protein toxin, melittin, destroys the insulating capability of the phosphoLipid layer without significantly altering the Bilayer structure. This Model membrane will allow the assessment of the effect of Lipid membrane perturbants on the insulating properties of natural Lipid membranes.