By using molecular dynamics simulation, the dynamic behaviors of particle permeation through a four-helix-bundle model channel are studied. The interior cavity of the four-helix-bundle provides the “routes” for particle permeation. The main structural properties of the model channel are similar to those that appear in natural four-helix-bundle proteins. It is found that the interior structure of the model channel may greatly influence the permeation process. At the narrow necks of the model channel, the particle would be trapped during the permeation. There is a threshold value for the driving force. When the driving force is larger than this threshold value, the mean first permeation time decreases sharply and tends to be saturated. Increasing the temperature of either the model channel or the particle reservoir can also facilitate the permeation. Enhancing the interaction strength between the particle and monomer on the four-helix-bundle model chain will hinder the permeation. Hence, the electrical current which is induced by the particle permeation is a function of the driving force and temperature. It is found that this current increases monotonically as the strength of the driving force or the temperature increases, but decreases as the interaction strength between the particle and monomer increases. It is also found that the larger the friction coefficient, the slower the permeation is. In addition, the multiparticle (or multi-ion) permeation process is also studied. The permeation of multiparticle is usually quicker than that of the single particle. The permeation of particle through a five-helix-bundle shows similar properties as that through a four-helix-bundle.
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8 March 2005
Research Article|
March 07 2005
Permeation of particle through a four-helix-bundle model channel
Bin Xue;
Bin Xue
National Solid State Microstructure Laboratory, Institute of Biophysics and Department of Physics, Nanjing University
, Nanjing 210093, People’s Republic of China
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Yu Su;
Yu Su
National Solid State Microstructure Laboratory, Institute of Biophysics and Department of Physics, Nanjing University
, Nanjing 210093, People’s Republic of China
Search for other works by this author on:
a)
Author to whom correspondence should be addressed. Electronic mail: [email protected]
J. Chem. Phys. 122, 104703 (2005)
Article history
Received:
June 11 2004
Accepted:
December 09 2004
Citation
Bin Xue, Yu Su, Wei Wang; Permeation of particle through a four-helix-bundle model channel. J. Chem. Phys. 8 March 2005; 122 (10): 104703. https://doi.org/10.1063/1.1854620
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