No abstract

The stability of the KcsA channel accommodating more than one ion in the pore has been studied with molecular dynamics. We have used the very last X-ray structure of the KcsA channel at 2.0-A resolution determined by Zhou et al. [Nature 414 (2001) 43]. In this channel, six of the seven experimentally evidenced sites have been considered. We show that the protein remains very stable in the presence of four K+ ions (three in the selectivity filter and one in the cavity). The locations and the respective distances of the different K+ ions and water molecules (W), calculated within our KWKWKK sequence, also fits well with the experimental observations. The analysis of the K+ ions and water molecules displacements shows concerted file motions on the simulated time scale (approximately 1 ns), which could act as precursor to the diffusion of K+ ions inside the channel. A simple one-dimensional dynamical model is used to interpret the concerted motions of the ions and water molecules in the pore leading ultimately to ion transfer.

Pore opening of KcsA channel is studied using targeted molecular dynamics simulations. Conformational changes of the protein are determined, starting from the crystallized refined 2.0 A structure (pdb 1K4C) determined in x-ray experiments and arriving to the open-state structure constructed on the basis of electron paramagnetic resonance spectroscopic data (pdb 1JQ1). Our results corroborate the essential role played by the terminal residues located on the transmembrane helices M2 which were not taken into account at that time. The aperture mechanism of the channel appears to be ziplike. A small constraint (approximately equal to 5 x 10(-2) kcal mol(-1) A(-2) per C(alpha)) applied to the terminal residues located on the intracellular side is sufficient to initialize the pore opening at the innermost part of the gate, but additional constraint must be applied to definitely complete the pore aperture. The open structure is proved to be a metastable state since releasing the constraint leads to another relaxed open conformation which seems to reach stability.