TY - JOUR
T1 - Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probed by 3D-RISM theory
AU - Phongphanphanee, Saree
AU - Yoshida, Norio
AU - Oiki, Shigetoshi
AU - Hirata, Fumio
N1 - Funding Information:
This work is supported by the Grant-in Aid for Scientific Research on Innovative Areas “Molecular Science of Fluctuations towards Biological Functions” ( 20107008 ) from the MEXT in Japan. NY is grateful for a Grant-in-Aid for Scientific Research ( 22740279 and 25410021 ) from MEXT, Japan , and to the Sumitomo Foundation .
Funding Information:
The authors thank for the discussion to Takashi Sumikama (Univ. Fukui). We are also grateful to the Next Generation Integrated Nano-science Simulation Software, the project of the ministry and the Strategic Programs for Innovative Research (SPIRE) and the Computational Materials Science Initiative (CMSI), Japan. Molecular Graphics images were produced using the UCSF Chimera package [39] .
Publisher Copyright:
© 2014 Elsevier BV. All rights reserved.
PY - 2014/12
Y1 - 2014/12
N2 - The potassium channel is highly selective for K+ over other monovalent cations, and the narrow pore structure with 3 Å in diameter named the selectivity filter (SF) is responsible for the selective permeation. Here we applied the statistical mechanics of liquids called three-dimensional reference interaction site model (3D-RISM) theory, and the binding configurations of the monovalent cations, Li+, Na+ and K+, with special attention on the contribution of water in the KcsA potassium channel were examined. All the three types of cations are bound in the open SF with high affinity, but with different binding coordinations: the in-cage configuration by eight carbonyl oxygens for K+, and the in-plane configuration by four carbonyl oxygens for Li+, whereas both configurations are allowed for Na+. In each case, water contributes an integral part of the ion coordination. In the case of Li+, a linear water-Li+-water complex is settled into two adjacent cages with the Li+ centered at the in-plane site. Positions of water around Na+ are more flexible, which may allow a transition between in-plane and in-cage configurations. K+ stably occupied in-cage configuration, and water occupies adjacent cages. The results provide the distinct configuration of ion and water in the SF, and serves clues for elementary process of selectivity.
AB - The potassium channel is highly selective for K+ over other monovalent cations, and the narrow pore structure with 3 Å in diameter named the selectivity filter (SF) is responsible for the selective permeation. Here we applied the statistical mechanics of liquids called three-dimensional reference interaction site model (3D-RISM) theory, and the binding configurations of the monovalent cations, Li+, Na+ and K+, with special attention on the contribution of water in the KcsA potassium channel were examined. All the three types of cations are bound in the open SF with high affinity, but with different binding coordinations: the in-cage configuration by eight carbonyl oxygens for K+, and the in-plane configuration by four carbonyl oxygens for Li+, whereas both configurations are allowed for Na+. In each case, water contributes an integral part of the ion coordination. In the case of Li+, a linear water-Li+-water complex is settled into two adjacent cages with the Li+ centered at the in-plane site. Positions of water around Na+ are more flexible, which may allow a transition between in-plane and in-cage configurations. K+ stably occupied in-cage configuration, and water occupies adjacent cages. The results provide the distinct configuration of ion and water in the SF, and serves clues for elementary process of selectivity.
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U2 - 10.1016/j.molliq.2014.03.050
DO - 10.1016/j.molliq.2014.03.050
M3 - Article
AN - SCOPUS:84915796628
VL - 200
SP - 52
EP - 58
JO - Journal of Molecular Liquids
JF - Journal of Molecular Liquids
SN - 0167-7322
IS - PA
ER -