Author(s): S. Furini, F. Zerbetto & S. Cavalcanti
Recent results of X-Ray crystallography have provided important information for
functional studies of membrane ion channels based on computer simulations.
Because of the large number of atoms that constitute the channel proteins, it is
prohibitive to approach functional studies using molecular dynamic methods.
overcome the current computational limit we propose a novel approach based on
the Poisson, Nernst, Planck electrodiffusion theory.
The proposed numerical
method allows the quick computation of ion flux through the channel, starting
from its 3D structure.
We applied the method to the KcsA potassium channel
obtaining a good accordance with the experimental data.
membrane protein, computer simulation, ion fluxes.
Ion channels are protein molecules embedded in the lipid bilayer of the cell
They control the ion fluxes through the cellular membrane playing a
central role in several cell functions, i.e.
the cellular excitability .
In the last
few years, thanks to the structural data provided by X-ray crystallography, it has
become possible to analyze the channels at atomic level.
In particular, the atomic
structures of several bacterial ion channels selectively permeable to potassium
ions - KcsA , MthK , and KvAP  - were revealed.
characteristic of potassium channels is the ability to conduct at a rate close to the
diffusion limit (108 ions/s) keeping a high selectivity (K+ is 104 times more
permeant than Na+).
Since high fluxes need conduction mechanisms without
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Paper DOI: 10.2495/BIO050111
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