Membrane molecular models

SENSORS BASED ON FREE-STANDING MOLECULARLY IMPRINTED POLYMER MEMBRANES. COMPUTATIONAL MODELLING OF SYNTHETIC MIMICKS OF BIORECEPTORS... 

Wiseman H, Cannon M, Arnstein HR, Barlow DJ (1992a) The structural mimicry of membrane sterols by tamoxifen evidence from cholesterol coefficients and molecular-modelling for its action as a membrane anti-oxidant and an anti-cancer agent. Biochim Biophys Acta 1138(3) 197-202... 

The second issue concerns the anisotropy of the membrane. The models presented in this section all assume that the membrane has the symmetry of a chiral smectic-C liquid crystal, so that the only anisotropy in the membrane plane comes from the direction of the molecular tilt. With this assumption, the membrane has a twofold rotational symmetry about an axis in the membrane plane, perpendicular to the tilt direction. It is possible that a membrane... 

This scenario for molecular packing leading to biased chiral symmetrybreaking is quite speculative. However, it makes an important point for molecular modeling of lipid membranes The unusual feature of diacetylenic lipids does not have to be associated with the stereocenter of the molecules but rather may be a broken symmetry in the packing of the kinks in the acyl chains. This speculation needs to be investigated by detailed molecular modeling calculations. 

One can apply the MC technique to the same molecular model, as explored in MD. One can use the same box and the same molecules that experience exactly the same potentials, and therefore the results are equally exact for equilibrium membranes. However, MC examples of this type are very rare. One of the reasons for this is that there is no commercial package available in which an MC strategy is combined with sufficient chemistry know-how and tuned force fields. Unlike the MD approach, where the phase-space trajectory is fixed by the equations of motion of the molecules, the optimal walkthrough phase space in an MC run may depend strongly on the system characteristics. In particular, for densely packed layers, it may be very inefficient to withdraw a molecule randomly and to let it reappear somewhere else in... 

Leermakers, F. A. M. and Kleijn, J. M. (2004). Molecular modelling of biological membranes. Structure and permeation properties. In Physicochemical Kinetics and Transport at Biointerfaces, eds. van Leeuwen, H. P. and Koster, W., Vol. 9, IUPAC Series on Analytical and Physical Chemistry of Environmental Systems, Series eds. Buffle, J. and van Leeuwen, H. P., John Wiley Sons, Ltd, Chichester, pp. 15-111. 

Figure 2.1 Exploded views showing the nonporous membrane size-exclusion phenomenon in the uptake and loss of organic compounds. Middle illustration shows the movement of contaminant molecules through transient pores in the membrane and retention (membrane exclusion) of much larger lipid molecules. Upper illustration shows similarly scaled space-filled molecular models of some organic contaminants and triolein, along with the hypothetical polymer pore (transient) size. Reprinted with permission from the American Petroleum Institute (Huckinset al., 2002).

This chapter gives an overview of the state of affairs in physical theory and molecular modeling of materials for PEECs. The scope encompasses systems suitable for operation at T < 100°C that contain aqueous-based, proton-conducting polymer membranes and catalyst layers based on nanoparticles of Pt. 

An alternative mesoscale approach for high-level molecular modeling of hydrated ionomer membranes is coarse-grained molecular dynamics (CGMD) simulations. One should notice an important difference between CGMD and DPD techniques. CGMD is essentially a multiscale technique (parameters are directly extracted from classical atomistic MD) and it... 

So far, CG approaches offer the most viable route to the molecular modeling of self-organization phenomena in hydrated ionomer membranes. Admittedly, the coarse-grained treatment implies simplifications in structural representation and in interactions, which can be systematically improved with advanced force-matching procedures however, it allows simulating systems with sufficient size and sufficient statishcal sampling. Structural correlations, thermodynamic properties, and transport parameters can be studied. 

Dai, R., Pincus, M. R., and Friedman, F. K. (1998) Molecular modeling of cytochrome P450 2B1 mode of membrane insertion and substrate specificity. J. Protein Chem. 17, 120-129. 

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