Porine simulations

Despite all the shortcomings listed above, full particle classical MD can be considered mature [84]. Even when all shortcomings will be overcome, we can now clearly delineate the limits for application. These are mainly in the size of the system and the length of the possible simulation. With the rapidly growing cheap computer memory shear size by itself is hardly a limitation several tens of thousands of particles can be handled routinely (for example, we report a simulation of a porin trimer protein embedded in a phospholipid membrane in aqueous environment with almost 70,000 particles [85] see also the contribution of K. Schulten in this symposium) and a million particles could be handled should that be desired. 

The simulation of ion channels and other pore-forming peptides and proteins at atomic detail is nowadays also possible. With the increase in computational power, these complex systems have attracted much more interest, and several simulations have been reported. Very often, only the transmembrane segments of the channel-forming proteins are included in the simulation to reduce the size and complexity of the system. The simulated systems range from synthetic model ion channels to a bacterial porine protein. 

The behavior of such a large system as a pore formed by a bacterial porine (E. coli OmpF) has been simulated in a lipid bilayer of palmitoyloleoylphosphatidylethanola-mine (POPE) [95]. Despite the use of united atoms, the final system of the trimeric porin embedded into 318 POPE molecules and solvated with water consisted of more than 65 000 atoms in total. During the 1 ns of the MD simulation the trimeric structure remained stable, with almost all flexibility in the loops and turns outside the 3-strands. The movement and orientation of the water molecules was investigated in detail. As found in case of the pore formed by the hexameric LS3 helix bundle [90], the diffusion of the water was decreased to about 10% of that of bulk water. Some ordering of the water molecules was evident from the average water dipole moments, which showed a strong dependence on the vertical position within the porine. 

Schirmer, T., and Phale, P. S. (1999). Brownian dynamics simulation of ion flow through porin channels./ Mol. Biol. 294, 1159-1167. 

Channel A Molecular Dynamics Simulation of OmpF Porin from Escherichia Coli in an Explicit Membrane with 1 M KCl Aqueous Salt Solution. 

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