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].
Revised: April 7, 2011 |
Published: February 6, 2007
Citation
Kariev A.M., A.M. Kariev, V.S. Znamenskiy, and M.E. Green. 2007. "Quantum Mechanical Calculations of Charge Effects
on gating the KcsA channel." Biochimica et Biophysica Acta--General Subjects.