The structure of the KcsA channel in ribbon representation, and the definition of the binding sites in the selectivity filter.
Initial configuration of the selectivity filter including ions and water molecules. A symbolic spring is attached to the last ion.
The location of water molecule . It mediates the bonding between Glu71-O-E1 and Tyr78-H-N. Two alternative conformations of the side chain of Glu71 are presented here. The switching motion of the side chain is induced by a water molecule leaking into the core part of the protein.
(Color) Upper part. Ion, water, and carbonyl trajectories in SMD1. The trajectories of ions K1, K2, and K3 (red); water molecules W1, W2 (cyan), W3 (blue), and W4 (green); and the carbonyl oxygens of the selectivity filter residues T-T-V-G-Y-G (black) are shown. Lower part: Orientational angle with respect to the pore axis for waters W1 and W3. The times of the translocation events are and for W1 and K2, respectively.
(Color) Time variation of the orientation, , of the carbonyl groups of TVGY.
(Color) The trajectories of ions K1, K2, and K3 (red); water molecules W1, W2 (cyan), W3 (blue), W4 (green), and W5 (cyan); and the carbonyl oxygens of the selectivity filter residues T-T-V-G-Y-G (black) are shown. Lower part: Orientational angle with respect to the pore axis for water W1 and W3.
The alternative conformations of the selectivity filter in SMD2. (a) The initial conformation of the selectivity filter. Only monomers M2 and M4 are shown here. (b) The alteration of the selectivity filter conformation. The amide hydrogen of Gly77 in M4 turns towards the pore axis and bound with a water molecule. The side chain of Asp80 changes its orientation and the binding between Glu71 and Asp80 is broken up.
The variation of the interaction energy before and after the first translocation in SMD1. The interaction energy between K2 and the carbonyl groups of Thr75, Val76, and Gly77 (top), between W1 and the carbonyl groups of Val76, Gly77, and Tyr78 (middle), and between W1 and K1 and K2 (bottom), are shown. The energy calculation includes the whole residue.
(Color) The pore potentials at different times : [(a) and (c)] for one ion and (b) for one water molecule. The open and full circles illustrate the average positions of the particles before and after their translocation, respectively.
Illustration of the geometry of a simple two-dimensional model of the KcsA selectivity filter.
(Color) The lattice potentials: (a) for a single ion and (b) for a single water molecule.
The interaction energy between a ion and a water molecule with different orientations as a function of their relative position . The “polarized bound state” at has an energy of .
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