Abstract
The electronic structure of the selectivity filter of KcsA K+ channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].
| Original language | English |
|---|---|
| Pages (from-to) | 292-301 |
| Number of pages | 10 |
| Journal | Biophysical Chemistry |
| Volume | 124 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - Dec 1 2006 |
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Keywords
- Bader charge
- Charge transfer
- First principles molecular dynamics
- KcsA
- Polarization effects
- Potassium channel
- Wannier centers
ASJC Scopus subject areas
- Biochemistry
- Physical and Theoretical Chemistry
- Biophysics
Cite this
Polarization effects and charge transfer in the KcsA potassium channel. / Bucher, Denis; Raugei, Simone; Guidoni, Leonardo; Dal Peraro, Matteo; Rothlisberger, Ursula; Carloni, Paolo; Klein, Michael L.
In: Biophysical Chemistry, Vol. 124, No. 3, 01.12.2006, p. 292-301.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Polarization effects and charge transfer in the KcsA potassium channel
AU - Bucher, Denis
AU - Raugei, Simone
AU - Guidoni, Leonardo
AU - Dal Peraro, Matteo
AU - Rothlisberger, Ursula
AU - Carloni, Paolo
AU - Klein, Michael L.
PY - 2006/12/1
Y1 - 2006/12/1
N2 - The electronic structure of the selectivity filter of KcsA K+ channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].
AB - The electronic structure of the selectivity filter of KcsA K+ channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].
KW - Bader charge
KW - Charge transfer
KW - First principles molecular dynamics
KW - KcsA
KW - Polarization effects
KW - Potassium channel
KW - Wannier centers
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U2 - 10.1016/j.bpc.2006.04.008
DO - 10.1016/j.bpc.2006.04.008
M3 - Article
VL - 124
SP - 292
EP - 301
JO - Biophysical Chemistry
JF - Biophysical Chemistry
SN - 0301-4622
IS - 3
ER -