Y. Wang, Y. Zenmei Ohkubo, and E. Tajkhorshid.
Gas conduction of lipid bilayers and membrane channels.
In Scott Feller, editor, Current Topics in Membranes:
Computational Modeling of Membrane Bilayers, volume 60, chapter 12, pp.
343-367. Elsevier, 2008.
WANG2008-ET
Exchange of gas molecules across biological membranes constitutes one of the most fundamental phenomena in biology of aerobic organisms. The primary mechanism for gas conduction across the cellular membrane is deemed to be free diffusion of the species across lipid bilayers, however, the involvement of a number of membrane channels in the process has also been suggested. In this paper we summarize the results of recent molecular dynamics simulations investigating the mechanism and pathways through which O2, CO2, and other biologically relevant gas species are exchanged between the two sides of the membrane. Several different computational methodologies, i.e., explicit ligand sampling where several copies of the gas species of interest are explicitly included in the simulation systems, under either equilibrium or biassed chemical potential conditions, as well as implicit ligand sampling where the distribution of small, neutral molecules inside membrane and/or a protein can be deduced from the simulation of the system without the ligand are employed.
The results of simulations of pure lipid bilayers indicates that although most bilayers are permeable by the gas species investigated, there is a significant barrier against gas permeation in the head group layer. The barrier appears to be, at least partly, due to a tighter structure of water in the head group region and can be affected by changes in the lipid composition of the bilayer. In addition to lipid bilayers, several membrane channels were also investigated. Interestingly, almost all studied systmes provide one or more pathways for gas conduction. Some of the identified gas conduction pathways are along the symmetry axis of oligomeric membrane channels, which might suggest a functional implication for oligomerization of these proteins inside the membrane.
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