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Title: Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel

Abstract

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K+ channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science 280 (1998) 69–77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106–109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523–526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed,more » configuration. This state shows four water molecules forming a “basket” under the Q119 side chains, blocking the channel. When a hydrated K+ approaches this “basket”, the optimized system shows a strong set of hydrogen bonds with the K+ at defined positions, preventing further approach of the K+ to the basket. This optimized structure with hydrated K+ added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The “basket” itself appears to be very stable, although it is possible that the K+ with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1–4].« less

Authors:
; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
917573
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochimica et Biophysica Acta--General Subjects, 1218-1229
Country of Publication:
United States
Language:
English
Subject:
08 HYDROGEN; AMINO ACIDS; ATOMS; CHAINS; CONFIGURATION; DIMENSIONS; FRICTION; HYDROGEN; OPTIMIZATION; OXYGEN; POTASSIUM; WATER; Environmental Molecular Sciences Laboratory

Citation Formats

Kariev, Alisher M., Znamenskiy, Vasiliy S., and Green, Michael E. Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel. United States: N. p., 2007. Web. doi:10.1016/j.bbamem.2007.01.021.
Kariev, Alisher M., Znamenskiy, Vasiliy S., & Green, Michael E. Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel. United States. doi:10.1016/j.bbamem.2007.01.021.
Kariev, Alisher M., Znamenskiy, Vasiliy S., and Green, Michael E. Tue . "Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel". United States. doi:10.1016/j.bbamem.2007.01.021.
@article{osti_917573,
title = {Quantum Mechanical Calculations of Charge Effects on gating the KcsA channel},
author = {Kariev, Alisher M. and Znamenskiy, Vasiliy S. and Green, Michael E.},
abstractNote = {The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K+ channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science 280 (1998) 69–77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106–109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523–526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a “basket” under the Q119 side chains, blocking the channel. When a hydrated K+ approaches this “basket”, the optimized system shows a strong set of hydrogen bonds with the K+ at defined positions, preventing further approach of the K+ to the basket. This optimized structure with hydrated K+ added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The “basket” itself appears to be very stable, although it is possible that the K+ with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1–4].},
doi = {10.1016/j.bbamem.2007.01.021},
journal = {Biochimica et Biophysica Acta--General Subjects, 1218-1229},
number = ,
volume = ,
place = {United States},
year = {Tue Feb 06 00:00:00 EST 2007},
month = {Tue Feb 06 00:00:00 EST 2007}
}
  • We have carried out quantum calculations on selected residues at the intracellular side of the selectivity filter of the KcsA potassium channel, using the published X-ray coordinates as starting points. The calculations involved primarily the side chains of residues lining the aqueous cavity on the intracellular side of the selectivity filter, in addition to water molecules, plus a K+ or Na+ ion. The results showed unambiguously that Na+ significantly distorts the symmetry of the channel at the entrance to the selectivity filter (at the residue T75), while K+ does so to a much smaller extent. In all, three ion positionsmore » have been calculated: the S4 (lowest) position at the bottom of the selectivity filter, the top of the cavity, and the midpoint of the cavity; Na+ is trapped at the cavity top, while K+ is cosolvated by the selectivity filter carbonyl groups plus threonine hydroxyl groups so that it can traverse the filter. Only one water molecule remains in the K+ solvation shell at the upper position in the cavity; this solvation shell also contains four threonine (T75) hydroxyl oxygens and two backbone carbonyls, while Na+ is solvated by five molecules of water and one oxygen from threonine hydroxyls. T75 at the entrance to the selectivity filter has a key role in recognition of the alkali ion, and T74 has secondary importance. The energetic basis for the preferential bonding of potassium by these residues is briefly discussed, based on additional calculations. Taken together, the results suggest that Na+ would have difficulty entering the cavity, and if it did, it would not be able to enter the selectivity filter.« less
  • Different ions in the pore of the KcsA channel behave differently, and we relate this to their solvation. We show that the selectivity is dependent, in part, on the solvation in the cavity (sometimes referred to as the vestibule, it is the region containing water molecules between the intracellular gate and the selectivity filter at the extracellular end of the pore). We have shown earlier that potassium is more dependent at the upper end of the cavity region on solvation by the threonines there, while sodium ion has more water molecules as ligands. In addition, sodium ion is placed asymmetrically,more » while potassium is nearly exactly symmetric with respect to the four-fold symmetry of the channel. We have now extended these calculations to rubidium and cesium ions, and find that rubidium solvation resembles that of potassium (and both are permeant ions), while cesium resembles sodium (and both are non-permeant), in terms of the geometry of up to eight hydrating, and four non-hydrating, water molecules. In each case, a maximum of 12 water molecules are relevant to the calculation. The placement of the water molecules in the two cases is essentially the same as found from the electron density in the X-ray structure of Zhou and MacKinnon. For Na+ and K+, we show that energy decreases from bulk to the cavity to the lowest position in the selectivity filter (accurate energy could not be calculated for the heavier ions). A separate calculation shows that fixing the Na+ ion at the position of the K+ minimum, followed by re-optimization produced a significantly modified system, not something that could be produced by thermal fluctuations. Moving the K+ into the Na+ position in the upper cavity led to a small increase in energy, ≈ 3 kBT, but was accompanied by large shifts in the positions of hydrating waters, which would create a major kinetic barrier. Therefore, thermal fluctuations could not invalidate the conclusions of the main calculations.« less
  • Using a constitutively active channel mutant, we solved the structure of full-length KcsA in the open conformation at 3.9 {angstrom}. The structure reveals that the activation gate expands about 20 {angstrom}, exerting a strain on the bulge helices in the C-terminal domain and generating side windows large enough to accommodate hydrated K{sup +} ions. Functional and spectroscopic analysis of the gating transition provides direct insight into the allosteric coupling between the activation gate and the selectivity filter. We show that the movement of the inner gate helix is transmitted to the C-terminus as a straightforward expansion, leading to an upwardmore » movement and the insertion of the top third of the bulge helix into the membrane. We suggest that by limiting the extent to which the inner gate can open, the cytoplasmic domain also modulates the level of inactivation occurring at the selectivity filter.« less