Abstract
We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 × 10-14 cm3/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures ∼12. This number is explained in terms of channel architecture and conduction mechanism.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 50-57 |
| Number of pages | 8 |
| Journal | Biophysical journal |
| Volume | 86 |
| Issue number | 1 I |
| DOIs | |
| State | Published - Jan 2004 |
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ASJC Scopus subject areas
- Biophysics
Cite this
Theory and Simulation of Water Permeation in Aquaporin-1. / Zhu, Fangqiang; Tajkhorshid, Emad; Schulten, Klaus.
In: Biophysical journal, Vol. 86, No. 1 I, 01.2004, p. 50-57.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Theory and Simulation of Water Permeation in Aquaporin-1
AU - Zhu, Fangqiang
AU - Tajkhorshid, Emad
AU - Schulten, Klaus
PY - 2004/1
Y1 - 2004/1
N2 - We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 × 10-14 cm3/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures ∼12. This number is explained in terms of channel architecture and conduction mechanism.
AB - We discuss the difference between osmotic permeability pf and diffusion permeability pd of single-file water channels and demonstrate that the pf/pd ratio corresponds to the number of effective steps a water molecule needs to take to permeate a channel. While pd can be directly obtained from equilibrium molecular dynamics simulations, pf can be best determined from simulations in which a chemical potential difference of water has been established on the two sides of the channel. In light of this, we suggest a method to induce in molecular dynamics simulations a hydrostatic pressure difference across the membrane, from which pf can be measured. Simulations using this method are performed on aquaporin-1 channels in a lipid bilayer, resulting in a calculated pf of 7.1 × 10-14 cm3/s, which is in close agreement with observation. Using a previously determined pd value, we conclude that pf/pd for aquaporin-1 measures ∼12. This number is explained in terms of channel architecture and conduction mechanism.
UR - http://www.scopus.com/inward/record.url?scp=0347946756&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0347946756&partnerID=8YFLogxK
U2 - 10.1016/S0006-3495(04)74082-5
DO - 10.1016/S0006-3495(04)74082-5
M3 - Article
C2 - 14695248
AN - SCOPUS:0347946756
VL - 86
SP - 50
EP - 57
JO - Biophysical Journal
JF - Biophysical Journal
SN - 0006-3495
IS - 1 I
ER -